I think it’s more of a deeper problem with language and reality more generally. To me it seems like species is a noun, like other nouns, but reality is ultimately a process. What is needed is a “verb-based” language for describing reality.
A lot of “process philosophers” like Whitehead, Deleuze, etc. have argued similar things.
So yeah I suppose I agree it’s ultimately a taxonomy problem, but in order to fix that I think you essentially need to reinvent language entirely. So it’s not a quick fix for biologists, it’s a systemic issue that I’m not sure really has a solution from within science itself.
I know this sort of doesn’t engage directly with your comment, but process philosophy is a personal interest and I wanted to link to the SEP, heh.
I’ll check out those books though, thanks.