The python recipes hand-maintains a RPROVIDES list for every package that it generates in native form (RPROVIDES=python3-email-native etc), so that dependencies work correctly when building native recipes. The manifest tool already knows this information so it should generate the RPROVIDES for us.
Pushing to 2.4 due to workload constraints.
Ross, this seems to be fixed in commit e720e3b4af036f0867f7616470013c714cad38e1 for scripts/contrib/python/generate-manifest-2.7.py and in commit 2f821f3c094927572fa599e3a07931b97073642e for scripts/contrib/python/generate-manifest-3.5.py unless you say otherwise, I will close this bug as fixed.
You're right, thanks for noticing.