Wouldn't the RBF need to pay more than the combined total from the separate transactions though ?
Yes, according to the current rules it need more coins. But one joined transaction will pay more than each of those two transactions are paying separately if we take satoshi per byte ratio. Imagine you have two transactions, each paying 1000 satoshi fee and each having 1000 bytes in size. Then, after doing cut-through on them, you can for example have one transaction paying 2000 satoshi fee and having 1500 bytes in size (because of cut-through). Then, from miner's perspective, including this one transaction is more profitable than including two separate transactions. Miner have nothing to lose, fees remain the same. However, as there is less space needed, such miner can fit more other transactions in the same block and receive more fees from that block.
If miners are mining for profit, they should quickly see that cut-through is working in favor of them and should activate such rules, because they will get the same amount of coins and they will need less space to include them in their blocks. Also, as they are RBF transactions, they don't have to be kept forever, finally only transactions included in blocks will be kept and the rest will be rejected forever as "provably never confirming transaction". Sooner or later, each miner by default will throw such transactions out of its mempool.
If the miner could make make more by adding the 2 separate transactions than the single cut through ?
No. Fees should remain at least the same to make sure that miner don't have to pay for having more space in a block. Miners shouldn't have a dilemma between transaction sizes and their fees, they should have an incentive to activate it (having the same fees occupying less disk space should be enough to convince them).
When there is only one transaction rbf works, since miner makes more.
When N transactions are joined into one, miner also makes more, because satoshi per byte ratio will be higher.
Only publishing the final cut-through txn removes any tricky decisions.
Yes. If transaction is confirmed, other transactions can be safely removed, as they are needed only to show other nodes that some replacement is not some double-spending attempt, but is honestly joined by cut-through.
