There are almost certainly such organizations, but they're different from the now-largely-extinct "craft" movement mentioned here. That was largely a phenomenon of the 2200s. Those guys - people like Muramune - built almost everything themselves apart from the really big-ticket items like antimatter reactors (or, well, presumably with a lot of automation, not actually by hand), they didn't start with an existing mass-produced starship.

It's kind of the difference between an organization that makes small-batch automobiles from the ground up, incorporating only a few production components like engines (Ascari, say), and one that does balls-out high-performance modifications of cars somebody else built (e.g. Brabus). The latter scene is alive and well in the 25th century. The former has, alas, largely died out.

--G.
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Benjamin D. Hutchins, Co-Founder, Editor-in-Chief, & Forum Mod
Eyrie Productions, Unlimited http://www.eyrie-productions.com/
zgryphon at that email service Google has
Ceterum censeo Carthaginem esse delendam.