Ideally, either the tub is set in notched studs or you fir out the walls so the cbu can come down over the tiling flange. But, that isn't done all that often, as the enclosure is normally a little large, and firring out the studs means the surround wall doesn't line up with the rest of the bathroom.
You should have a vapor barrier behind the cbu that laps over the tiling flange. This could be plastic or roofing felt. If the cbu won't install over the lip, you can bring it down to just above the lip. As long as the tile you're using is supported by more than half on the cbu, the overhang of the tile by the lip won't be a problem. You want a small gap at the tile/tub joint, and you should caulk that. Personally, and industry, when you have a deep joint like that, it's better to first partially fill it with foam backer rod, then caulk. The caulk then gets shaped more like an hour-glass and can flex better without pulling itself off of one edge or the other when installed as a big rectangular slug of caulk. And, when it comes time to recaulk, you have a better chance of getting the old stuff out.