I sort of understand the rationale behind timing plays, and 4th out appeals that led us here, but isn't this particular fix incredibly simple?
A runner leaving 3rd without tagging up is neither out, nor scored.
If the fielding team throws to 3rd, or appeals within the rules, then they are out.
If the baserunner returns to 3rd before leaving the field of play, then properly scores, the run counts.
If a 3rd out if recorded before either of those things, it doesn't matter. No run, no out.