The thing is, starbases get linear benefits from research, while mobile ships get exponentially better. A late game fleet with all upgrades doesn't just have 20% better damage and 30% better defense, it is also much, much bigger, because of additional fleet supply. In the "attacking fleet vs. defending starbase" matchup, both sides benefit the same amount from weapon and defense upgrades, but the fleet can become several times more powerful by researching fleet supply and building more ships, while a starbase will never be more powerful than 8 upgrade slots' worth of toughness.
It could work out that a fully-upgraded starbase would be tough enough to hold the line until reinforcements arrive even against a lategame 200-ship attack fleet, but then you just get the reverse problem - you can get fully-upgraded starbases before then, so they would be completely invincible against mid-game fleets.
High-tier tech that gives an automatic bonus to every starbase would help solve this problem. It would bridge the gap between the mid-game, when you reach the point where you can afford a fully-upgraded starbase, and late-game, when fleets are so big that even upgraded starbases don't cut it.
And again, some things just aren't worth a module, but might become a valuable strategy if you could just get them from research. The Advent culture upgrades aren't terrible as far as culture spread goes, but culture is a secondary supporting mechanism, not something you can rely on to win the game. It's easier to get culture by building the normal logistics structures. Anyway, if you wanted to build an enormously expensive orbital structure that gives you cultural power as Advent, you could build a Deliverance Engine.
So starbase culture modules don't make much sense; if they were changed to be good enough that you'd want to buy them, then starbases would be stealing the superweapon's thunder. But unless the upgrades are that good they aren't worth building, since culture isn't a strong enough strategy to justify spending logistics slots AND starbase slots unless it will really steamroll someone. On the other hand, if you could get some culture spread/suppression from starbases for free after doing some research, you might think, "OK, I'm going to build starbases and have culture anyway, so now I can try to make these two things work together. Researching this tech helps me do that."