Firefox OS is dealing with similar compromises with homescreen site icons and the apple touch icons.

https://bugzilla.mozilla.org/show_bug.cgi?id=921014

Even though sites should be using the standards version the Apple one is still very popular. If you decide not to support it, users just think your OS / Browser looks like crap. It's a tough spot to be, especially considering that its financially in Apple's best interest to break the web.

EDIT: Linked to wrong bug