You’ve raised an interesting concern. It makes a lot of sense so far, for the purposes of non-trivial & convenient editing. The idea I’m getting is you want to highlight a specific pitch range (or pitch classes) that may or may not be varied horizontally. But I hope you can elaborate otherwise.
The next update of SP will feature a lasso tool for grabbing notes more precisely, and for avoiding adjacent notes easily (provided you have an Apple Pencil). This should come in handy for what you described.