As far as I know, you can't do that using Relationship Finder. However, if you want to check to see if you (or someone else) are a direct descendant from a particular person, without relying on the questionable ancestor, you can use Ancestor Listmaker to do that. Just use the app to generate a list of ancestors back to at least the person you want to check your descent from and click on the ancestral lines link next to that person's name. That will show you a page with ALL your lines of descent from that person so you can see if there are any that don't go through the questionable ancestor.
does it make a difference if the parents are marked as "uncertain"?
will the Relationship Finder honor that setting? (you might have to wait 24 hours or more for a re-index if recently modified)
The Connection Finder on Wikitree+ can do it. See G2G post Full Connection finder on WikiTree+. In my March 11 "answer", Aleš explains how to do it.