It's hard to tell from the pic but it's critical that the flange doesn't protrude past the Hardibacker.
Next, even though it's flashed there is still a gap between the Hardibacker and the flange. That should be sealed.
Further, it looks like you have the new, waterproof Hardibacker? If so, how do they require that the seams and penetrations are sealed? That might be what you want to use to seal that gap.
Finally, one of the drawbacks to installing Hardi above the flange is just what you've run into. You'll have to start with a full tile around the flange and you'll probably only be bonding about an inch or maybe 1.5 inches of the tile.
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