Have there been any changes in this regard with the time of Bitcoin Core 0.16? Then it was done well and all OK nodes accepted the second transaction with a higher Commission first, and the old one was forgotten later and discarded
Not really, RBF was already available before Bitcoin Core 0.16 but it wasn't turned on for every transaction by default. If you increase your transaction fee using RBF, you decrease one of your output's value; you don't add new ones or remove them completely. Such transaction replaces the old one without any problems. However, just as I described above, if you create another transaction spending the same inputs but with completely different outputs then most nodes by default will reject such transaction.