> So the miner doesn't get paid in fees but in a normal transaction
Correct
> neither can the miner mine a second transaction into the same block, spending the payment transaction mostly in fees
I'm less sure about that part. When the miner sweeps the money from Swap Address A, he's perfectly allowed to pay dust (or less) to his "real" address and use the rest of the utxo as a transaction fee. But if he does that, it will be a pretty clear fingerprint that will allow chain analysts to identify Swap Address A as a swap address. For best privacy, the miner should gradually spend the money in Swap Address A in transactions that look relatively normal.
> he can do that to pay out future swaps to ramp up the coinbase transaction
Yes, I hope that the extra revenue they make ends up increasing the relative size of coinbase transactions, which should make mining pool members happy
> But that could also muddy these pristine UTXOs
How would it muddy them? I suspect there are ways miners can use a utxo to contribute to the coinbase via a series of transactions that look perfectly normal, in a way that I don't think chain analysts can't easily detect