blotunga: They extend your range and territory. Isn't that enough? I think they also can be used for repairing ships but I'd have check the code to make sure.
Brasas: That sounds quite nice. How to use them then? Must the transport be carrying materials? Or maybe it needs to be done on system with colonizable planet?
I'm fairly sure I clicked that Outpost option, for some turns the transport looked like it was doing something, and then the transport was just there normally and no Outpost that I could see...
In addition to what blotunga said: Multiple (& more developed) transports speed up the building process. You always loose one transport (they are the materials needed ;) ), no entire fleet, so don't worry that you might loose 5 transports at once. Besides the obvious extension of space they are good border markers for your empire & tough fortresses: single ships usually do not stand a chance. If they work like in "ST - Birth of the Federation" the biggest starbases actually require small fleets to be removed. Or a borg cube.
BTW: does the game has a variant of the borg cube? I remember it a major pain in the butt & guaranteed fleet losses (except for Romulans, a solid fleet could decloak-alphastrike it away without losses). With a bit bad timing that thing was a session ender.