The article touches on it - assuming it's correct, it's because they did a bunch of proprietary modifying on Mono, so it's not "just" Mono any more, it's Mono and a decade or more of the most exciting layer violating crimes you can imagine.

I would assume, if someone Meta scale had an app that had to be built on Unity for whatever reason, we'd see similar blogposts to the ones they did about finding bespoke optimizations for their Android app to be performant with how enormous it became, probably involving either some bespoke alternative to IL2CPP, or writing a bunch of bespoke optimizations onto a bastard descendant of whatever version of Mono Unity originally derives from and so supports...or just paying Unity so much money they get to do whatever they want to the underlying source.

I’ve heard (but don’t have an inside source) that Meta’s Horizon was built on Unity and then ported to a custom engine implementation.