The tags were needed for language indication to control CJK glyph variants. Flag emoji were grafted onto this scheme. The key is that tag sequences have to start with a valid introductory codepoint. Simple enough to strip out anything that isn't a flag.

> Simple enough to strip out anything that isn't a flag.

But it's not simple enough for every company/app to independently research the entire Unicode code point space (which is MASSIVE) to find out what kinds of "fix ups" that app needs to do to clean the data it consumes.

It's complicated or at least has difficult tradeoffs. Maybe you invest a lot of time carefully surveying all of the Unicode planes and decide which ones you care to keep unchanged and which ones you filter/strip. For every code point you reject or change, there is going to be some user who is confused or dissatisfied with the limitations of your app.