I believe you're missing ac29's point. Android allows applications to distinguish between cached data and "regular/permanent" data. It also allows users to clear them separately.

Logically, the Apple ID / phone number mapping seems like it should fall under cached data (e.g. it can be regenerated and does need to be re-checked from time to time). If the iOS Messaging app properly implemented this distinction, users (or Apple) could clear this cached mapping without touching anyone's message history. Sadly, it sounds like it hasn't been implemented that way, so...