Well, the long and short of it is, you will have to build the variants you desire individually in MML first.
You will have to use a year that Omnis are available, so these won't be 3025 units in terms of MHQ mechanics, so you'll have to ignore unit years to use these in 3025. Don't forget to mark the "Omni" box next to the Mech's tonnage!
When you build your prime variant, give the Chassis a name and use "Prime" in the Model window. You will need to use the CHASSIS name for all variants, but you then save each weapons layout with whatever name you wish to give the variant in the MODEL window. These Model names will then show up as available refits within the MHQ proper when you want to refit to one of those.
Finally, make sure you save each of your layouts in the data/mechfiles/custom folder and refresh your unit cache!
I also discovered that if you want to turn a stock 3025 cached Mech into an Omni you will have to change all its components from Fixed to pod-mounted. Go to the Assign Criticals tab and right-click on each item to change them from Fixed to pod-mounted.
I did some Commando versions. I'll paste them here. Note that the CHASSIS name is Commando3025O.
Commando3025O Prime
Mass: 25 tons
Chassis: Coventry Metal Works
Power Plant: GM 150
Cruising Speed: 64.8 kph
Maximum Speed: 97.2 kph
Jump Jets: None
Jump Capacity: 0 meters
Armor: Lexington Limited
Armament:
8.0 tons of pod space
Manufacturer: Coventry Defense Conglomerate,Coventry Metal Works,Vandenberg Mechanized Industries,Rim Motors
Primary Factory: Coventry,Coventry,Illiushin,Otisberg
Communication System: TharHes Crystal Flower RG-2
Targeting & Tracking System: TharHes Star Shark
Introduction Year: 3145
Tech Rating/Availability: E/X-X-X-D
Cost: 2,364,063 C-bills
Overview
Created for the Lyran Commonwealth Armed Forces and one of the first 'Mechs ever designed for reconnaissance, the Commando was much lighter and faster than its precursors, though it still utilized primitive BattleMech technology.
Capabilities
With only four tons of armor to protect itself, the Commando is not meant to participate in a stand-up fight against heavier enemies, but it excels at hit-and-run tactics and as a scout hunter.
Deployment
The standard COM-2D Commando carries two different SRM launchers, a Coventry 4-tube and a Shannon Six Shooter, each with one ton of ammo. The secondary weapon is a Defiance B3M Medium Laser. This weapons load can cause a lot of damage for a light 'Mech and makes the Commando an effective striker, especially when used in groups. An often-used tactic for those is to rush upon a single target, concentrate their fire and retreat before the enemy can offer effective resistance. The COM-2D's communication gear, Crystal Flower RG-2, as well as the Star Shark targeting system were produced by TharHes on Tharkad.
History
In 2463 Coventry Metal Works (then known as Coventry Defense Conglomerate) introduced their second BattleMech, the COM-1A Commando. The Commando was able to destroy much heavier Kuritan Gladiators during the first large-scale battle between BattleMechs in 2475 on Nox. The installed Large Laser caused several problems and other 'Mechs were soon introduced (like the Wasp in 2464 and the Stinger in 2479) that were better equipped for scouting and even mounted jump jets. The Commando's profile was radically changed with the introduction of the sophisticated COM-2D variant in 2486, which exchanged the laser weaponry with short range missiles and turned the machine into a striker. The Commando became popular among LCAF forces and, nearly 600 years later, is still mainly in use by Lyrans. The Commonwealth went to great pains to keep the 'Mech solely in Lyran hands, especially during the years of the Star League. It took an alliance with the Federated Suns and the creation of the Federated Commonwealth to break the stranglehold. The Commando was chosen as the standard light BattleMech for the Armed Forces of the Federated Commonwealth next to the Valkyrie, and after the upgrade to the COM-5S model in 3050, Vandenberg Mechanized Industries was allowed to produce the old COM-2D for the Taurian Defense Force. Furthermore, the Marian Hegemony deploys the Rocket Launcher-packed COM-4H, and the Word of Blake produced its own variant (the COM-7B) during its occupation of Coventry from 3068 to 3074.
Type: Commando3025O
Technology Base: Inner Sphere (Standard)
Tonnage: 25
Battle Value: 541
Equipment Mass
Internal Structure 2.5
Engine 150 Fusion 5.5
Walking MP: 6
Running MP: 9
Jumping MP: 0
Heat Sink 10 0
Gyro 2
Cockpit 3
Armor Factor 64 4
Internal Armor
Structure Value
Head 3 6
Center Torso 8 8
Center Torso (rear) 4
R/L Torso 6 6
R/L Torso (rear) 3
R/L Arm 4 6
R/L Leg 6 8
Weight and Space Allocation
Location Fixed Space Remaining
Head None 1
Center Torso None 2
Right Torso 2 Heat Sink 10
Left Torso 2 Heat Sink 10
Right Arm None 8
Left Arm None 8
Right Leg None 2
Left Leg None 2
Right Arm Actuators: Shoulder, Upper Arm, Lower Arm, Hand
Left Arm Actuators: Shoulder, Upper Arm, Lower Arm, Hand
Weapons
and Ammo Location Critical Heat Tonnage
SRM 6 CT 2 4 3.0
SRM 4 Ammo (25) RT 1 - 1.0
Medium Laser LA 1 3 1.0
SRM 6 Ammo (15) LT 1 - 1.0
SRM 4 RA 1 3 2.0
Notice there are 2 fixed heat sinks in each of the LT and RT. This is because the 150-rated engine only hides 6 of the 10 basic heat sinks, so the other four have to be fixed.
Commando3025O L
Mass: 25 tons
Chassis: Coventry Metal Works
Power Plant: GM 150
Cruising Speed: 64.8 kph
Maximum Speed: 97.2 kph
Jump Jets: None
Jump Capacity: 0 meters
Armor: Lexington Limited
Armament:
8.0 tons of pod space
Manufacturer: Coventry Defense Conglomerate,Coventry Metal Works,Vandenberg Mechanized Industries,Rim Motors
Primary Factory: Coventry,Coventry,Illiushin,Otisberg
Communication System: TharHes Crystal Flower RG-2
Targeting & Tracking System: TharHes Star Shark
Introduction Year: 3145
Tech Rating/Availability: E/X-X-X-D
Cost: 2,416,406 C-bills
<snip TRO entry>
Type: Commando3025O
Technology Base: Inner Sphere (Standard)
Tonnage: 25
Battle Value: 731
Equipment Mass
Internal Structure 2.5
Engine 150 Fusion 5.5
Walking MP: 6
Running MP: 9
Jumping MP: 0
Heat Sink 10 0
Gyro 2
Cockpit 3
Armor Factor 64 4
Internal Armor
Structure Value
Head 3 6
Center Torso 8 8
Center Torso (rear) 4
R/L Torso 6 6
R/L Torso (rear) 3
R/L Arm 4 6
R/L Leg 6 8
Weight and Space Allocation
Location Fixed Space Remaining
Head None 1
Center Torso None 2
Right Torso 2 Heat Sink 10
Left Torso 2 Heat Sink 10
Right Arm None 8
Left Arm None 8
Right Leg None 2
Left Leg None 2
Right Arm Actuators: Shoulder, Upper Arm, Lower Arm, Hand
Left Arm Actuators: Shoulder, Upper Arm, Lower Arm, Hand
Weapons
and Ammo Location Critical Heat Tonnage
2 Small Laser CT 2 1 1.0
2 Small Laser RT 2 1 1.0
Medium Laser LA 1 3 1.0
2 Small Laser LT 2 1 1.0
4 Medium Laser RA 4 3 4.0
Commando3025O J
Mass: 25 tons
Chassis: Coventry Metal Works
Power Plant: GM 150
Cruising Speed: 64.8 kph
Maximum Speed: 97.2 kph
Jump Jets: Standard
Jump Capacity: 180 meters
Armor: Lexington Limited
Armament:
8.0 tons of pod space
Manufacturer: Coventry Defense Conglomerate,Coventry Metal Works,Vandenberg Mechanized Industries,Rim Motors
Primary Factory: Coventry,Coventry,Illiushin,Otisberg
Communication System: TharHes Crystal Flower RG-2
Targeting & Tracking System: TharHes Star Shark
Introduction Year: 3145
Tech Rating/Availability: E/X-X-X-D
Cost: 2,510,156 C-bills
Type: Commando3025O
Technology Base: Inner Sphere (Standard)
Tonnage: 25
Battle Value: 614
Equipment Mass
Internal Structure 2.5
Engine 150 Fusion 5.5
Walking MP: 6
Running MP: 9
Jumping MP: 6
Heat Sink 10 0
Gyro 2
Cockpit 3
Armor Factor 64 4
Internal Armor
Structure Value
Head 3 6
Center Torso 8 8
Center Torso (rear) 4
R/L Torso 6 6
R/L Torso (rear) 3
R/L Arm 4 6
R/L Leg 6 8
Weight and Space Allocation
Location Fixed Space Remaining
Head None 1
Center Torso None 2
Right Torso 2 Heat Sink 10
Left Torso 2 Heat Sink 10
Right Arm None 8
Left Arm None 8
Right Leg None 2
Left Leg None 2
Right Arm Actuators: Shoulder, Upper Arm, Lower Arm, Hand
Left Arm Actuators: Shoulder, Upper Arm, Lower Arm, Hand
Weapons
and Ammo Location Critical Heat Tonnage
2 Small Laser CT 2 1 1.0
3 Jump Jet RT 3 - 1.5
2 Small Laser RT 2 1 1.0
3 Jump Jet LT 3 - 1.5
2 Small Laser LT 2 1 1.0
2 Medium Laser RA 2 3 2.0
Basically just the L version swapping medium lasers for jump jets.