I think you can use a combination of both - keep league position as the primary factor, but give the higher placed team a goal headstart in any playoff game for every "x" points they finished ahead (maybe 6,8 or 10 perhaps)So if a team finishes a certain amount of points ahead of a team that should rule out the play offs? It shouldn’t go by league positioning but by points difference? People wouldn’t moan about that?
It’s a football league, it has to have rules, they have to be fairly simple, if you want the play offs, which most sensible people who are not fans of a lot of dead rubber fixtures do, you need cut off places by positions, which will always be a fairly blunt tool but, as I said, you know before the season starts where you stand.
Not only would it reflect a tangible advantage for the team doing better over the whole season, it would also encourage clubs in the playoff zone to keep pushing to the last day to maximise/minimise the gaps to their potential playoff opponents.