Short answer: no, unless alex puts a bunch of work in (unlikely)
Long answer: This would put a lot of work on modders to make this work as you want, unless alex puts a bunch of work in to make this possible/easy.
Say for example you want just the ships from a mod, and none of the weapons.
it's almost 100% likely that the modder used the weapons from the mod on some/all of the variants for the ships, as such those variants will not work as you have disabled the weapons, this will cause crashes (unless alex adds some system that autoconverts variants "broken" by only loading part of a mod to use an appropriate available weapon instead)
To do this without requiring alex to program a new "variant conversion system", and "just" add a set of tickboxes to enable/disable parts of a mod, then modders would have to make multiple variants for ships that do/don't use weapons from their mod, and that would be a lot of work for larger mods. And i expect some modders wouldn't bother with supporting this feature anyway, for various reasons.
This would also have the potential to completely break faction mods, as an example:
If you decide "i want to use Kyeltziv, but just for the ships and disable all the weapons"
Then you'll find that the Kyeltziv faction will suddenly not know how to make any weapons as i've not set them to know any of the vanilla weapon BPs.