A VERY large part of it is rule of cool and suspension of disbelief, but there are a few possible explanations. Not all planets are inhabitable but still possess good resources so they could be strip-mined(but as they're not inhabited and its worthless once this is done, there's no territory on the board itself), harvesting asteroids within the territory's system for materials, transmuting worthless materials to useful ones(for magical or VERY high tech races, though technologically its not very efficient). Going further on the transmuting one, for a magical Empire, you could in theory gather enough mages to simply magic the necessary materials for a ship. Very cheap and godmod-ey method, especially given the whole "Wait, if I have magic, why the hell should I even work as part of a Empire? What could these people do for me I cant do for myself?" angle if we just magic up whatever we want, BUT still possible with how SP's magic system works. Then you have races like the Lorcar that work differently on a fundamental level. The way I explain them is they just attack non-spacefaring or even yet intelligent races offscreen for biomass or collecting the necessary elements and compounds from dead planets to process into biomass(the only reason I haven't explained this on the forum before is nobody's asked). The reason you dont often see this played out IC if our respective Empires actually do them is because most of these just aren't really that interesting to play out(at least in my opinion, anyways).
