It could easily be more streamlined. Simply make refit points generate at the same time as resource points. I know the logic they applied is that all other benefits are useable for a turn so arrange the management phase to make that true of repair yards too.
But in early game, repair yards are hands down, no question the most valuable strategic benefit and it isn't even remotely close. Do they really need to make the management phase clunky just to ensure repair yards are the unquestioned master of benefits? Would you avoid them if there were a chance your opponent could take them back before you reaped the benefit?
Diplomats are garbage mostly. They're useable as very late game campaign point denial, but might as well not exist early to mid game.
Skilled spacers are no guarantee. They're only useful if you're defending a world that has standard objective cards. If you're behind on campaign points, playing on worlds with fixed objectives, defending a base, or defending a special assault they're unusable. If you have a stranglehold on spacers, the opposing team can mitigate their power or sidestep it entirely if they want.
Spynets are great, but there are 3 of them and they're only on worlds with low resource/campaign point value (average 3.7 resources, 0 campaign points per location).
Repair yards have an average resource value of 12 (not including the refit) and 1.5 campaign points. Also repair yards benefit every team member equally whereas every other benefit must be divided amongst players.
So is it really necessary to have an internal loop in one phase just to make sure the best benefit becomes the best-est-er? No.
They could've also sidestepped the wonkiness by allowing you to IMMEDIATELY build a base after a victory if you've got a spare 15 RP in your coffers. No looping phases, and the opportunity to reap immediate rewards if you set aside funds for investment.
From a narrative aspect, not being able to use repair yards until the following turn makes sense. Wouldn't a yard have to familiarize itself with ship schematics, acquire compatible machinery, and order parts to fix up a ravaged ship of the line? Imperials need triangle bits, and Rebs need lumpy bits, a constant changing of hands would lead to near constant parts shortages, no? "You're out of isosceles?! What! I've got deadlines dammit!"