No, that wasn't my understanding (the bolded part doesn't follow from what's said above, does it?). Fees aren't subject to penalty at all. The penalty depends purely on size of block (if I understand correctly). Even if the tx fee was payed out of band, the tx will still contribute to the penalty through increased block size. Yes, it's deducted from the tx fees (can be other tx fees), but it depends (in amount) on the fact that the tx takes up space in the block.

In other words: it's not the fee that's penalized (neither in block nor out of band), but the space it takes up in the block.

Again: if I understand correctly.

EDIT: regarding the discussion about what happens with block reward going to 0: this means that you can't mine a block with only transactions that had their fees paid out of band, because they would take up space and thus effect a penalty, but there'd not be enough on-chain fees to pay for it.