I commiserate on the issue with later economic starbase upgrades. It's the diminishing returns decision. I went through some similar angst when approaching the new system. The summary is that I let my planets auto upgrade and control it by when I research what. The same thing seems to be applicable to the starbase modules. You possibly manage your planets strictly manually and are looking to extend that to starbases. Turning off the automatic update in the sponsor settings is possible and I tried that for a while, but was able to talk myself into the autoupdate with some exceptions and it is working.
I think the best thing for you and several others with similar concerns is an easy way to set the default settings for the sponsor settings dialogue. You would want that setting to be manual by default. I would like the requested constructor to be specific design by default, one I can change as technologies and situations change. Others would have different choices for different reasons. But doing it starbase by starbase is the kind of prohibitive micromanagement the system was designed to avoid.
I find that the same thing is true with the Govern Colony screen with its automatic update settings and that different people have different ideas of what is proper default. I think those defaults should be easily managed as well for very similar reasons.
I suggest the idea of little templates or profiles that can be selected, but am open to any technique that addresses this part of the management system. Obviously, it is most applicable to those of us with big maps, but it should be helpful to everyone with any OCD approach to the game.