Do you sync your desktop vault with iCloud?
Then this should solve your issue:
This should make it possible to add .nosync to your .obsidian folder on desktop and then choose this as the vault config folder. iCloud won’t sync it to your mobile vault and you can have your .obsidian there. I suppose it will get synced to the desktop as well, but because you use another folder there, you should be safe.
If that answers your question, please mark this as the solution. Thank you!