The com.apple.developer.parent-application-identifiers entitlements are both added automatically to the app clip target on creation.
Xcode doesn't seem to add the corresponding com.apple.developer.associated-appclip-app-identifiers entitlement to the parent app target.
I added it (manually) to the parent app's entitlements file, with the value $(AppIdentifierPrefix)com.myproject.Clip, and it seems to work. Didn't get another ITMS-90876 error email from App Store Connect after submitting.