I wouldn't put Logan as a guarantee of being in the post DOFP happy ending universe. It is basically its own thing.
Mangold said it was. The whole point of setting it in 2029 was to create some distance between in the ending of DOFP and Logan. If Logan was in its own world, then adding that gap of time wouldn't matter in the first place.
You get to hear him as Two-Face in Lego Batman, though. Not a bad consolation prize.
Didn't he have just one line?