Ah yes, Natwest does that (or did, at least, the last few times I had to help a family member). You’re right, not showing warnings when it’s a regular payee would be a no-brainer; as well as reducing the annoyance for such transactions, it would also emphasise that they’re context-sensitive and therefore should be paid attention to when they appear.
I wonder how much of this is down to lazy programming*, where it’s easier to say “do this for every payment” than all the different things for different conditions.
*To be clear, not meaning to imply individual programmers are lazy, as this could be down to how the product is budgeted for or the conditions drawn up when it was scope, meaning it is, or is the consequence of, a management-level decision.