First things first. This mod is pretty much standard if you have the Plentiful Traditions that it's based upon, with several powerful ascension perks that really are worth the minor hassle of fixing the mod. So! Onto fixing the mod...

The easiest place to start is at the Paradox Launcher, & clicking on the options "..." to then select "open in file" to use your file browser to actually open up the mod folder associate with this mod.

Open up "common" then open up "static modifiers" where you'll find a file named "00_static_modifiers", or "00_static_modifiers.txt" if your browser is set up to show you file extensions. Double click it & it should default to Notepad.

Upon the Notepad window, hit ctlr-F if you're on Windows, to find instances of 'starbase' quickly. You'll pretty much immediately find the two relevant entries you need to delete, as they specify that all starbases, regardless of level, now have -2 modules, -5 buildings.

If you have a game already going, your starbases are now usable, & you have access to a large number of interesting & powerful perks upon ascension. You just have to spend some starting alloys to fill in the gaps. Meanwhile, your starting home system starbase will have its proper beginning modules & building.

Thanks go out to @RedHistorian for pointing out the offending lines for this guide.