This seems like yet another example of people not understanding what we are actually doing.

No, I thought it was the former, but it had me questioning a bit. Technically the scenario of paying more for bigger shares would not be logical as the guy/gal/dog who submits the winning share would get a larger percentage of the proverbial pie.
I don't understand every nuance, my specialty is hacking and fixing the mining hardware. That I'm good at :-)
Technically, the guy/gal/dog who submits the winning share DOES get the larger percentage of the proverbial pie, or at least used to, in the form of a 0.5% incentive. I don't know if that's still coded in or not though.
From the P2Pool Wiki:
A subsidy of 0.5% is sent to the node that solved the block in order to discourage not sharing solutions that qualify as a block. (A miner with the aim to harm others could withhold the block, thereby preventing anybody from getting paid. He can NOT redirect the payout to himself.) The remaining 99.5% is distributed evenly to miners based on work done recently.