This version of this P.R. rule jumped out at me, too. And what you layed out is where I also wound up with it. The why of xp bonuses and, especially, penalties is something I don’t get.
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I think the bonuses for prime requisites are there to encourage you to play an archetype based on your ability scores e.g I'm strong so I'll be a fighter. The 'virtual' reallocation from other stats gives you a bit of differentiation and reward for having another above average ability - the fighter's strong but also smart so advances faster.