This idea of "rational value" you think is incoherent is perhaps a straw-man. Let's instead say that some people think that those methods you are using to discard instrumental values as irrational or find/endorse arational terminal values, might be generalized beyond what is obvious, might assume mistaken things, or might be an approximation of rules that are more explicitly justifiable.

For example, I think a lot of people use a simple line of reasoning like "okay, genetic evolution led me to like certain things, and memetic evolution led me to like other things, and maybe quirks of events that happened to me during development led me to like other things, and some of these intuitively seem more justified, or upon introspecting on them they feel more justified, or seem from the outside as if there would be more selection pressure for their existence so that probably means they're the real values, ..." and then basically stop thinking, or stop examining the intuitions they're using to do that kind of thinking, or continue thinking but remain very confident in their thinking despite all of the known cognitive biases that make such thinking rather difficult.

Interestingly very few people ponder ontology of agency, or timeless control, or the complex relationship between disposition and justification, or spirituality and transpersonal psychology; and among the people who do ponder these things it seems to me that very few stop and think "wait, maybe I am more confused about morality than I had thought". It seems rather unlikely to me that this is because humans have reached diminishing marginal returns in the field of meta-ethics.