Clan BattleMechs and IIC variants of IS Mechs, which are often a different tonnage than their IS original version mind you, should be allowed full customization just as IS BattleMechs are.
PGI will have to simply stamp down their hardpoint inflation urges and not give them more hardpoints than they come with, that alone will be enough to keep them from being easily OP'd via customization.
The Hunchback IIC, 2 ultra20s and 2 ermeds, a Mech assignment that meant you have seriously messed up and your superiors want you dead, because while you may get a kill with this Mech, you shouldn't survive the encounter. Keep the 2 ballistic and 2 energy hardpoints, leave it at that. Still leaves plenty of room to customize the Mech and allow it to be something other than the punishment it was originally meant to be. There are other variants of the Hunch IIC that include 4 ERL(not enough sinks to deal with the heat) as well as ATMs and even a Clan Rotary AC variant, for later on down the road. Since the Hunch IIC is only 50 tons, same as the original Hunch, allow it to be considered a Hunchback for Skill Tree purposes, so you don't have to get 3 Hunch IIC variants to Master it.
Most of the IIC Mechs are similar, they are redesigns of original IS Mechs, some are actually either lighter or heavier in tonnage than their original IS counterpart however. For the IICs that aren't the same weight, they would probably need to produce 3 variants so you can Master them.
http://www.sarna.net/wiki/IIC is a good source for the IIC Mechs.
Also keep in mind, there are C variant Mechs that the Clans produce after taking over IS facilities, these are standard IS Mechs using Clan Tech, not redesigned Mechs, just refits essentially. These would IS chassis's using Clan Tech on them, and those could also be added in a few years as the Clans start producing them. And keep in mind, after the Truce, the Clans SELL these C class Mechs to the IS, along with OmniMechs and other tech.....