Basically this is by design, but it might make sense to consider this case:

1. Build any project.
2. Disabled automatic signing and a select a provisioning profile.
3. Build in Unity and use append on the generated project:

The provisioning profile remains the same, but the 'Team id' is overridden to an empty string (assuming it's not set in Player Settings), this is bad because in manual mode the team cannot be changed (it's read only) and only changes when the profile is selected.

I guess it would make sense to either override both fields or not set team id when appending or we could only set the team id if the string is not empty?