I understand what you're saying. Occurrences like https://en.wikipedia.org/wiki/Ring_species demonstrate that the idea of "species" isn't firm and that what truly matters is each individual and their unique circumstances. But this seems to me to be more a limitation of language and philosophy than a repudiation of math.
As you pointed out, it's all equivalent to drawing tally lines, counting pebbles, sliding counters on an abacus, or counting fingers and toes. Despite the fractal nature of coastlines and the constant exchange of matter and energy between adjacent parts of the universe, it is possible to agree upon useful delineations. And there is not any alternative maths which happens to describe practical observations in a way which does not reduce to the maths with which we are familiar.