Its actually been said that PUTs are to be paid for with MDs. But the actual specifications have not been explored by the team yet, but it has been said that MDs are different in this regard.
Guess I should now go looking for the statement.
Here @frabrunelle mentions that MD updates maybe chargeable and the rate to be worked out. SAFEcoins though are handled differently and not charged for but perhaps if the user sets the ledger bit that ledger entry will have to be paid for.