I have filed FB22791285 regarding this.

Please everyone file feedbacks, the more Apple gets for the same issues, the more likely we'll receive a fix! Mine is FB22686646.

I agree, we should be able to handle this. FB22686646

I started having this issue about 10 hours ago FWIW, on a provisional and on a paid developer account. I am unable to build for physical devices.

In reply to @DTS Engineer: I am able to build my app with a new bundle ID, but not the already existing bundle ID. I am unable to confirm if also adding a capability fixed anything as I did this at the same time as changing the bundle ID unfortunately. However, I still have issues that I want to build my app with the current bundle ID.

After making sure the permission was on for the executable to access the folder, restarting my Mac fixed it for me. Appears that the permissions is not adhered to until the restart. Edit: still getting the message, unfortunately. I wish it could be overridden for a specific executable.