Uglies are meant to be the result of scrapping ships and essentially kitbashing them together. By that note, it makes more sense for recycling factions to produce them, as they would logically be the people cleaning up after the battles and have the parts to make them. Uglies are not made from scratch like medical ships, and all the others. hence the distinction.
Shall this in the future also reflect like I can take the wings from a N1 Starfighter, cockpit from a Sleuth, and sublight-engines from an I-Beam? Because right now I build from scratch a beautiful ugly made of ore that was in the soil of a planet a week ago. ;p
It is unclear from the Dev Plans available whether the manufacturing process will ever be added-to in order to use Ships (or wrecks of ships) instead of RMs in the manufacturing process for uglies. My guess is no, that's not planned, but it's a fun idea.