This is a config option ported over from DINUM's Sydent: https://github.com/matrix-org/sydent/pull/285
They've switched to validating 3PIDs via Synapse rather than Sydent, and would like to retain this functionality.
This original purpose for this change is phishing prevention. This solution could also potentially be replaced by a similar one to https://github.com/matrix-org/synapse/pull/8004, but across all `*/submit_token` endpoint.
This option may still be useful to enterprise even with that safeguard in place though, if they want to be absolutely sure that their employees don't follow links to other domains.
Andrew Morgan