Okay, so there’s an option in Settings > Input named “Menu Swap OK & Cancel Buttons”, which is enabled by default on the Android build. This makes navigating RetroArch consistent with MAME4droid, which is nice but a fairly significant change as far as the out-of-the-box experience goes.
I had a quick look on the forums but can’t find an existing thread on this; couldn’t see it in the release notes either. After updating the Android version from 1.3.6 to 1.4.1, this confused the hell out of me for a good half an hour. Just posting this here for the record, in case anyone else got caught out by it.