I assume you're recalling mods like Factorization or Railcraft (bottling machine, blast furnace, etc)? It'd be interesting to be able build a structure out of multiple blocks, turning it into a modeled machine, but I have trouble imagining that in Starmade's current state. The game is kinda designed for you to build systems in whatever scale you wish.
This could scale for StarMade. You'd basically place a large frame or enclosure of arbitrary size based on how large of a system you wanted, and then build the walls and other parts. The system could even be more advanced, with certain placement rules for certain modules and other things. I wouldn't mind this sort of mechanic rather than the blob-anywhere systems we have now, but it would put certain restrictions on ship designs that people might not like.
(Additionally, this doesn't seem like the sort of thing that development should be focused on. Systems really just need to be functional, balanced, and flexible in terms of ship designs allowed. Beyond that, what you do with those systems - missions, faction mechanics, exploration... - are the main thing to think about now IMO)