I was able to get it working borrowing from @DTS Engineer 's approach but with specific entitlements files per build configuration. So using the xcconfig files he mentions do something like:
APP_CLIP_ENTITILEMENTS = myProject/myProject.entitlements then specify $(APP_CLIP_ENTITLEMENTS) under Code Signing Entitlements in Build Settings
and just create different entitlements files for each project.
I also tried the full suggestion above beforehand and couldn't get it to work as it doesn't seem like Xcode interpolates the variables in the entitlements file (but it would be nice if it did! certainly nicer than copying entitlement files in this specific case).