No the desktop and iOS app syncs for me perfectly with Mac Mini M2 Pro / OS 26.4
Try upgrading to the latest iOS version 10.4.5188 just out a few days ago in the App Store and see if that makes any difference.
If the new updated IOS version still makes no difference, then see my posts in the following thread below for more information, where another user also had eg: deleted emails on the desktop that were not synching the same to the iOS app
I’ve noticed an issue with my Mail app syncing between devices. When I mark emails as read or delete them on the macOS version (26.4) eMv (10.4.4867 (a1d5549), those changes aren’t reflecting on my iOS device (26.4) eMv(10.4.4899 (74ed093).