Since release 2.9.0, spells assigned to modified buttons (LT+X, RT+Y, etc) no longer show flyout icon on cooldown, or on spell/proc alert

Pretty sure this isn't actually a bug, so could you share a screenshot of what you mean?

Sorry, is it a new setting or something? I've been looking extensively through the new settings and I can't see where that was added. I assumed it was a bug because the 2.9.0 release notes don't mention it.

What I mean is that in 2.8.x, if you used a spell that was assigned to LT+X and it went on cooldown, then while in the neutral view (LT not depressed) the LT+X flyout would be visible (showing the spell cooling down) until the spell was no longer on cooldown.

In 2.9.0 that's no longer the case - spells assigned to modified buttons no longer fly out while on cooldown. I can share a screencap if you want but it'll just be of the neutral button bar view; there's nothing to show because spells on cooldown no longer trigger the flyout.