I have no idea why they recommended moving away from native, it’s not explained there… afaik you need native for some proton variants, that’s why there are two packages proton-cachyos and proton-cachyos-slr
The topic was unceremoniously closed without further explanations.
It gives you the option because it is installed.
Someone tested it in the announcement thread and said the native version runs better, like it theoretically should.