If I uncheck sections in the screen options GUI, does WP still try to update the associated post meta within that section?
This won’t speed up saving, that markup needs to be generated otherwise JS can’t show/hide it on the frontend.
On top of that, the data still needs to be saved, but wether that happens is plugin specific. Eitherway this isn’t a good route to go down if your saving is slow.
Instead of speculating, actually measure what’s happening when you save a post using a plugin such as query monitor, or profiling such as XDebug or XHProfile. You might be surprised by what you find ( e.g. making remote requests is super expensive ). Also consider reducing the number of plugins.
Note that while you didn’t clarify if you were talking about the Block editor, or the classic editor ( or a page builder ), this applies to all of them.