Lyle: I believe the intent of the Par+4 penalty is to give the offending player a relatively stiff penalty. If you set Par based on MPO play, then that penalty for MPO players is about four throws vs. their division. But with MPO Par the effective penalty for lower divisions is probably closer to only one or two throws vs. their division. Punishment for the same offense should carry the same weight, but in this MPO-set-Par-for-everyone scenario it doesn't.
As someone pointed out upthread you can eliminate this problem by making missed holes a DQ instead. But I don't think the PDGA wants to be that strict, e.g. Sarah Hokom car crash at 2015 Worlds.