Managing plugins with the engine built from source?

Hi! I would like to make my engine build more lightweight, and first step is probably to remove a bunch of plugins that I don’t need and will never need, E.G the python plugin takes 30gb.
However, what is the correct method of managing these plugins? Obviously I do not have a “Manage plugins” button to delete or install new ones like in the epic launcher. Is it safe to just delete them?
I also got an issue where if I disable a plugin in my project, the engine can no longer start on it’s own, E.G to generate a new project, as it complains about not finding the files for the plugin i disabled. Surely the engine should be standalone? Or are source builds different and intended to be on a per project basis?

Any other tips on how to make it more lightweight?