For FrikBot you could alternately create a separate ".way" file for the map, if you don't want to bake those entities into the map.
I've never tried FrikBot waypointing myself, but the docs at
https://www.insideqc.com/frikbot/fbx/readme.html have a "Waypointing" section that describes using an in-game editor to create and then dump out the waypoints. You can choose to dump them in a format for ".way" files, or as entities to include in your map, or even as QuakeC if you wanted to handle the waypoints in mod code (but IMO don't do that).
I wouldn't bother with other bot support I think. Nobody makes Omicron bot routes these days, and I think Frogbot pretty much requires baking the routes into QuakeC code.