I think you may be misunderstanding my point. It's not a "burden" on the penalized player, it's a disservice to the rest of the lower skilled division. And relatively (to skill) speaking it's not equally applied to all players.
If you're setting par based on MPO level play and have a difficult "Par 3" hole on which MPO's average a 3... then a penalized MPO player is carding 4 throws over the divisional average. But look at the MA4, FW3, or MJ4 divisions... they're probably averaging 5's on that same "Par 3" hole and penalized players are only carding 2 throws over the divisional average. You can probably find extreme examples where an FJ6 player scores better than the divisional average by taking a Par+4 penalty on the hole.
For tournament play by PDGA rules the only thing Par matters for is taking that Par+4 penalty. As long as that's the case there should be divisional par for tournament play.
To make sure I understand, you think the penalty should be, say, four strokes over what someone of the said players ability can score on the hole? That is, a pro on a par 2 would get six strokes, and a rec might get eight strokes since rec players average four on the hole.
If so, you're correct, I did misunderstand you. That said, I still disagree. 1) you are going with the supposition that a player, in theory, has little say in how they play a hole. Beyond the fact that isn't necessarily correct, as you've pointed out, a player has absolute say in whether they arrive on time, or if they play the course correctly. To me that is the mitigating factor. If you are talking about a situation where the player has absolutely no ability to impact the situation, and he is treated differently than the other player, then I agree. But that isn't the case here. 2) The imposition of par + 4 is equivalent across that player's division. It impacts that player as much as every other player in the same fashion. If the notion is that it is harder/easier for a pro to make up the difference, than a lower ranked player, well, that's not true. A pro has to make up that difference against other pros, who shoot at the same level he does. So does the am player. Relatively speaking the punishment is the same, steep, but not insurmountable.
On the other hand, setting par correctly has more meaning by what you've laid out. If the hole is set at par 3, and it is actually par 2, then the pro who misses it has been given an extra stroke that his competitors will never get. If that is part of your argument that I've missed, yes, I strongly support your position.
Last, honestly, I don't have a good enough feel for this to worry too much about it. It's easy for me to debate it, but the only way I'd really want to weigh in would be if someone had real numbers on the impact. Doing it the way you would like doesn't seem unfair, just cumbersome. If asked to vote on it, I would pass.