We have cannon examples. Stone's forces captured the production lines AND the technical data packages for the Bolla Stealth Tank. Thus, we get the RoTS Bolla, with C3, a 4 ton troop bay and more pod space.
The Bolla is an extremely rare exception, and done because Stone evidently really wanted a stealth tank for his spec op forces, plus his forces neatly had the plans and the factory. Most of the Blakist special gear (eg Celestials) got destroyed.
If we ever hear of the Homeworld Clans, we might get another exception: The Osteon. The TWOR supplemental notes that it is being investigated for continued production if the Nova CEWS can be removed, but the writeup notes that it is rather integrated into the chassis so the 'Mech is banned for now...
I will note that in-universe, modifying a 'Mech may not be as simple as rules make it. Consider the Avatar: with BMM, it gained perk "Stabilized Weapon (CT medium lasers)". So, the weapons are in stabilized mounts. Rules-wise, upgrading them is simple factory job. In-universe... well, are ER Medium Lasers identical to standard lasers? It might be that the mounts would need to be modified to fit ER types there, and that might require other modifications, causing a cascade of modifications, and everything needs to be tested. Might not be worth it.
Likewise, the Osteon. Rules-wise, removing the Nova CEWS is simple, in-universe evidently not so.