In GC2 shiptemplates could hold functional modules - however, only for their outward design, they were actually without function (*). So, essentially, one could use all available mods - functional or not - to make a design without any limitation whatsoever.
That this is not possible right now because of blablabla is just a lame excuse - the game could simply be coded to work like the prequel did and that would be the best solution, and given the fact that the code already exists it shouldn't be that difficult.
(*) Actually there was a minor function - if the auto-designer would pick weapons or defenses on a template it would use the anchors of the void non-functional weapon/defense modules and replace them with working ones. This was, again, a good solution, otherwise the autodesigner would have to place all these in random order at anchors (which could happen at some time, eg. if current miniaturization level would exceed the number of real weapons vs. the proxy-weapons) and that would lead to chaotic designs.