Clones can develop their own features and go their own way. I don't think calling something a clone is necessarily rude.
At some point it will be significantly different that it probably shouldn't be called a clone though, but if it currently has the same name as a feature in a pre-existing, popular software, "clone" seems like the right word.
I imagine whomever built "bottles" (the clone, not the Crossover feature), probably used code, or at least was inspired by code, that CodeWeavers upstreamed to Wine.
At some point it will be significantly different that it probably shouldn't be called a clone though, but if it currently has the same name as a feature in a pre-existing, popular software, "clone" seems like the right word.
I imagine whomever built "bottles" (the clone, not the Crossover feature), probably used code, or at least was inspired by code, that CodeWeavers upstreamed to Wine.