I chalk it up to manufacturer markup.
Seems more that this explanation is papering a pretty noticeable crack. I mean, why don't the individual weapons on the aftermarket have any kind of markup? Same weapons, same price list.
But you can avoid the manufacturer markup by buying the Mech with the cheapest loadout, and then fitting aftermarket parts. Even with the technician costs, it will be cheaper.
What makes it worse is that the Omni markup (which can be attributed to the cost of the pod, weight balancing, etc) scales on the same tonnage formula. A Medium Laser costs 80,000 as an aftermarket part. If you apply an aftermarket Omni cost it is 100,000.
That same ML on a 20 ton regular Mech costs 96,000. On a 100 ton regular Mech it costs 160,000. If you Omni those, 20 ton costs 120,000 (80k x 1.25 x 1.2) whilst 100 ton costs 200,000 (80k x 1.25 x 2).
Same weapon, different costs depending on what you attach it to. And it doesn't make sense.
Now, the formula has components we can look at. Structure, Weapons and Equipment, Omni, Tonnage. Now it makes sense that the Omni cost and the Tonnage cost are applied to the Structure. Tonnage modifier for bigger Structure? Yep, I understand that. OmniMechs are more complex, and so more costly? I agree.
Omni cost to Weapons and Equipment? Absolutely. Again, you pay for the complexity. Tonnage modifier? You pay more for the same equipment depending on what it is attached to? Nope. Don't get it.
Unless the tonnage modifier is paid when you buy aftermarket parts as well, it doesn't make sense to apply it to the build at the time. And since you can swap weapons from one Mech to another regardless of tonnage, without paying for the cost difference, it doesn't make sense for the tonnage modifier to apply to weapons at all.
So I would suggest that a new formula is used where there is a tonnage modifier.
(Structural Cost x (1 + [Total Tonnage / 100]) + Weapon/Equipment Costs) x (Omni Conversion Cost*)
This way the tonnage modifier applies to the structure, and the Omni cost applies to both the weapons and structure.