Hi! This isn't an issue, the rotation is set that way for a reason of Blender and game engines using different coordinate systems and โupโ axes, which causes orientation mismatches when exporting the 3d assets.
I purposely set the rotation that way, so there wouldn't be a mismatch when importing them to Unity.
The Godot, and Unreal engine devs have never reported having an issue because of this.



In the inspector window, you can see that the original model's mesh has the 90 deg rotation applied. Godot recognizes that this is not zeroed out, so there is a small 'undo' icon that will let you click on it to zero it out. If you do, the actual mesh will have this orientation:
