For most things in the real life that we categorize, the rules that distinguish those categories can be vague. It doesn't mean those categories are not valid, or a function of 'human perception'.
We have difficulty with biological distinction, but we can still confidently categorize something as being a 'Horse' and 'Not A Horse' ... even if sometimes it's a little bit ambiguous, aka 'Kind of a Horse'.
Edit: and as for 'other ways of thinking' it very quickly goes into metaphysics so it's hard to talk about because we don't spend much time in that realm. 'Emergence' and 'Biocentrism' are interesting ideas (fields?) that sit within more or less regular bounds of science and so they're just examples of what I'm referring to.
I think you'd have to define what it means for a category to be valid. The way I see it is that a category is either useful or not and whether it is or not depends on our goals which depends on what we like and want which is subjective and the judgement itself relative to such a system so designed. That's not to say they are arbitrary, because they're objectively useful or not with respect to the goal.
I don't think biologists would agree with you about the horse. It's actually consider a crisis in the philosophy of biology that the concept of species is ill-defined. [1] Like I said, the resolution to me is pragmatic: the definition will depend on whether it is effective relative to some purpose.
A biologist would only take umbrage rhetorically, which is fine, but they'll never categorize a rock, a flower, or a human as 'a horse' so in reality it's not a problem.
While 'value' is surely in the eye of the beholder ... whether or not something fits into the category is not as subjective.
And frankly, the 'big question' is 'who is the beholder' - which is something that materialism is struggling to tell us.
Interesting and plausible, but you didn't give an argument or any example for that.