When I cut and paste from a searchable .pdf, Scrivener is capitalizing the beginning of each line. I think it’s because it’s reading a hard return at the end of the previous line, but regardless, I don’t want it to do that!
Have you tried turning off the ‘Fix capitalization of sentences’ within Edit > Options > Auto-correction tab?
I think it’s just the way Scrivener works with new lines, as you’ve said, and if you turn that option off just while you copy/paste, hopefully that should work.