Ah, the part I love most about making dou - getting the shape perfect and finding out that there’s a sizable gap.
Simply put, the surface of one of those pieces (or both) have to be shaved so they fit closer. Of course, when you change one corner, all the other corners get affected when tightened together.
There’s good news and bad news, and they’re both the same. There’s no secret trick, you just have to simply shave down the problem areas until they all fit closer. Work slowly and carefully. Very little wood actually needs to be removed, but it does need to be removed in such a way where all the corners line up. It’s just a matter of working slowly and observing/thinking how shaving one corner will affect the rest.
The closer the pieces, the more solid the joint will be. However, it doesn’t need to be perfect. Above all, do the best you can. After you give it all you’ve got, whether achieving flush joints or back to where you started, you can go from there.
Currently, I think that gap is a little too big to use filler, but if you manage to get them a bit closer, it could be doable.