It's probably due to the way it's implemented. One of the programmers can correct me if I'm wrong here, but when the assembly is made, it probably sets the non-moddable flag on it so that it can't be modded. What whizkid 2 does is change that to another flag, the single mod flag, that allows 1 mod to be added on (usually used for specific unique items). In order to allow all assemblies to have a single mod on, the game would probably have to check all of your items (and every item on the ground) to find the assemblies (which, by the way, are not specially marked to my knowledge) and change the flags around. I'm sure it COULD be done, but it seems like it would be a lot of work.
E: A quick glance at the item flags shows that there is in fact one for assemblies. It would still have to check every item in the level, inventory, and equipment for assemblies.