Did some testing: seems like your technological research bonus is separate. Your researched slots are respected.
If you have a lot of things in your inventory so that your inventory is expanded then you keep the bonus slots when you uninstall. But if you empty your inventory (and have the bonus setting low enough that your inventory isn't expanded when your inventory is empty) and then uninstall then you have the correct amount of slots.
So you can easily do safe uninstalls with no leftover bonus from the mod if you just make sure your inventory size is regular at the time.