Redguard can do well for the cement board itself. But it alone is not adequate for that cement board/tub flange joint.
If the cement board were installed over the flange as is typical, with a small gap caulked with silicone or the like, and the cement board Redguarded, that would work. The overlap gives a shingling effect. I don't think Redguard will stick to the tub (not sure) or reliably bridge the current gap (quite sure). So as is, water will run down the Redguarded cement board, hit the gap, wick around the bottom edge of the Redguard, and get to the framing.
It looks like the flange is flush with the face of the cement board in some of your photos. That can happen if the framed opening is a little too big for the tub; it should be a tight fit on 3 sides. The usual way to address that is to fur out the framing as required so that the backside of the cement board is in plane with the face of the flange. That way the cement board can hang down and overlap the flange, as designed, while still remaining flat.
Furring and rehanging the cement board would be one solution to the current problem. It would also require resetting the shower valve to the proper depth to account for the furring. But it sounds like that may be required anyway, because I agree it looks quite wonky.
Cheers, Wayne