I have the Mini 3 Pro, but the issues are the same.
When I load the image set into PTGui they get placed according to the meta data which is a nice start, as they are roughly in the right place.
My next step it to select from the Control Points menu, "Generate Control Points for all overlapping images". That way it only looks for points where points will be, so less chance of false positives from on overlapped images.
Now you can hit "Align Images". In most cases that will give you good alignment.
Here's a tip for the zenith gap. For reasons known only to DJI the Sphere function shoots the whole sequence in landscape mode, when in fact the camera is capable of capturing the zenith, completing the sphere when in portrait mode.
So what I do is take two photos manually before or after the sequence with the camera in portrait and the gimbal tilted fully up to 60 degrees. The two pictures are 90 degrees yaw apart. Add those and your zenith is covered.
For the very best results, shoot the whole sequence manually, this lets you use AEB or 28MP resolution (not both) and fully manual settings. It just takes a while to do.
The biggest issue I have is that PTGui can't handle the vignette you get from the DNG files. The vignette curve works to an extent to reduce it, but doesn't remove it by any stretch.
I end up having to convert to Tiff pre-stitch which is a bind.