Ok, so I think you can consider most of these as optional since the availabilities involved are very low-frequency. That being said, this should be the complete list of 'Mechs whose availability in these RATs diverge from the listed MUL availabilities. So if you are aiming for complete synchronicity...
(I actually managed to find quite a few errors in my own notes in this process, too...)
I only managed to compare for 3028, 3039 and 3050. A lot of these are rare Intro-level tech, so it'd require me to do significantly more research to see what could plausibly still be around post-Clan Invasion.
I put my best guess at an availability rating (using the values from the tables in the PDF) for 'Mechs where the MUL implies something should be added.
Light 'Mechs
Flea FLE-14 -- remove everywhere (extinct in MUL)
Locust LCT-1E -- add to all factions who don't already have it for 3028, 3039, 3050 (and likely later) [Av = 1 to 3]
Thorn THE-N -- remove from DC in all years (looks like it is listed for DC in Hist:3039 but retconned in TRO-3039 to DC having only the THE-S and THE-T, and MUL goes with TRO... the A* RAT in Hist:3039 looked like it has multiple errata after further review)
Commando COM-1B -- add to Lyrans in 3028, 3039, and 3050 (unclear later) [Av = 1]
Commando COM-2D -- add to Merc/Periph Gen, OWA, MoC in 3028 [Av = 1 to 2]
Falcon FLC-4N -- remove everywhere (only available to WD and Comstar and extinct by Civil War)
Hermes HER-1A -- remove from all but FWL in 3028, 3039, 3050 (and most likely later)
Hermes HER-1B -- remove from all but FWL in 3028, 3039, 3050 (and most likely later)
Valkyrie VLK-QA -- add to Taurians in 3028 [Av = 1 or 2]
Jenner JR7-D -- add to all factions who don't already have it for 3028, 3039, 3050 (and likely later) [Av = 1 to 3]
Panther PNT-9R -- add to all factions who don't already have it *except FWL* for 3028, 3039, 3050 (and likely later) [Av = 1 to 3]
Medium 'Mechs
Assassin ASN-21 -- add to CC in 3028, 3039, and 3050 (and likely later), and add to SIC in 3039 [Av = 1 or 2]
Sentinel STN-3K -- add to DC in 3028 (ok in other years... turns out they had some pre-Myndo) [Av = 1 or 2]
Hermes II HER-2S -- add to CC, DC, MoC in 3028, 3039, and 3050 (and likely later) [Av = 1 or 2]
Centurion CN9-A -- add to MoC, OWA, Taurians in 3028 [Av = 1 or 2]
Centurion CN9-AH -- add to all factions who don't already have it for 3028, 3039, 3050 (and maybe later) [Av = 1, maybe 2 for some]
Centurion CN9-AL -- add to all factions who don't already have it for 3028, 3039, 3050 (and maybe later) [Av = 1, maybe 2 for some]
Cronus CNS-3M -- remove from CC in 3039, 3050 (and most likely later)
Kintaro KTO-18 -- add to DC and/or DC-A* in 3039 and 3050 (and most likely later ...apparently they got both the upgraded and Intro tech variants from Comstar) [Av =2 or 3]
Scorpion SCP-1N -- add to Lyrans in 3028, 3039, and 3050 (not clear if later) [Av = 1]
Gladiator GLD-3R -- technically remove from all but Merc/Periph General in 3028, but honestly, I'd rather see it updated in the MUL to have IS-General availability for the LSW and Clan Invasion eras, if you can pull any strings with Team MUL ;) It's technically consistent with either outcome, as they are with "planetary militias and low-tier mercenary commands" (TRO:SW)
Gladiator GLD-4R -- same issue/lobbying request as for GLD-3R
Heavy 'Mechs
Champion CHP-2N -- remove from MoC, OWA, and Taurians, and maybe Merc/Periphery Gen, too (available to Mercs in MUL, but not Periph-Gen)
Dragon DRG-1C -- remove from Merc/Periph Gen (available to DC and FRR only, extinct by Civil War)
Merlin MLN-1A -- remove from all Houses in 3028, 3039, 3050, and 3057 (only Merc and OWA availability in MUL thru 3061, then rest of Periphery only)
Catapult CPLT-C1 -- add to Merc/Periph Gen, MoC, OWA, and Taurians in 3028 (available to all in MUL) [Av = 1 to 3]
Guillotine GLT-4P -- remove from CC, DC, FS, Lyrans in 3028, 3039, 3050, and 3057 (only available to FWL, Mercs, and all Periph in MUL, then extinct by Civil War)
Orion ON1-V -- remove from MoC and OWA in 3028 (only Taurians and Marians have it in the MUL)
Orion ON1-VA -- remove from MoC, OWA, and Taurians, and maybe Merc/Periphery Gen, too (available to Mercs in MUL, but not Periph-Gen)
Assault 'Mechs
Awesome AWS-8T -- remove from MoC, OWA, and Taurians, and maybe Merc/Periphery Gen, too (available to Mercs in MUL, but not Periph-Gen)
Awesome AWS-8V -- remove from MoC, OWA, and Taurians, and maybe Merc/Periphery Gen, too (available to Mercs in MUL, but not Periph-Gen)
Charger CGR-1A1 -- add to FWL in 3028, 3039, and 3050 (and maybe later) (don't know what they did to deserve this...) [Av = 1]
Goliath GOL-1H -- remove from DC and FS in 3028 and 3039 (keep 3050 and later) (diffuses to all factions starting in 3050 in MUL)
Striker STC-2C -- remove from all but CC, SIC, and Lyrans in all years
Thug THG-11E -- remove from DC-A* in 3039 only (must get refits from 3050 forward)
Striker STC-2C -- remove from all but CC, SIC, and Lyrans in all years
Crockett CRK-5003-0 -- remove from DC in all years (extinct by Late SW era; DC also doesn't have CRK-5003-1 just in case it's a typo. They only get the Katana)
Cyclops CP-10-Q -- remove from MoC, OWA, and Taurians, and maybe Merc/Periphery Gen, too (available to Mercs in MUL, but not Periph-Gen)
Atlas AS7-RS -- all to all factions who do not have it in 3028, 3039, 3050 (and likely later) (available to all in MUL) [Av = 1 to 3]
