It's all just wildly unrealistic space fantasy anyway, so it doesn't bother me that some handwavery explanation is given for why space fortresses make sense - if it benefits gameplay. That being said, I don't think the fortress aspect of starbases works very well. A bastion starbase with a full complement of defense platforms is extremely expensive to build and maintain compared to how quickly it gets melted by even a medium-size fleet. I suspect they are weak on purpose to reward aggression and to avoid the AI getting stuck in space trench warfare forever.
If they wanted bastions to be more useful as defensive chokepoints, they'd need to be able to actually hold out until a fleet arrives, have a garrison fleet at very low cost (defense platforms are expensive and slow to build) and/or require special ships to handle them.
Big space fortresses with doom weapons and the ability to somehow be relevant are a cool part of space opera. I'd prefer having fewer starbases, but having them more distinct, with a choice of developing them into much more dedicated roles: research stations, bastions, grimdark space prisons, training facilities, trade hubs, shipyards, etc. The upgrades slots don't really do this job, they're just min-max variables, and the difference between stations are tiny.
This ties into my main issue with Stellaris in it's current incarnation: I don't mind too much the simplified FTL mechanics, the shift towards space mana and the very gamey peace/war exhaustion mechanics. But I do feel that there is very little choice in how to develop planets and stations - they're all very generic and the tile bonus mechanic is terrible, imo, in the way it's tiny bonuses everywhere, rather a few big bonuses. Races also don't vary much apart from a few % here and there. It gets very much generic spacemans on generic space colonies with generic space stations and generic space ships.
It does seem like the desire to achieve balance gets in the way of having mechanics, choices and differences that actually matter. Space Opera should be about archetypes and extremes. Stellaris is a good game in many ways, but also deeply flawed due to this strange fear of unbalancing the game.