I think the formal similarities of some aspects of arguments about qualia on the one hand and rationality on the other, are the extent of the similarities. I haven't followed all the recent discussions on qualia, so I'm not sure where you stand, but personally, I cannot make sense of the concept of qualia. Rationality-involving concepts (among them beliefs and desires), though, are absolutely indispensable. So I don't think the rationality issue resolves into one about qualia.

Rationality uncontroversially involves rules and goals, both of which are naturalisable. You have said there is an extra ingredient of "caring", which sound qualia-like.

What you ought to do is distinct from what you will do.

Not in all cases surely? What would an is/ought gap be when behaviour matched the ideal

Natural science can tell you at best what you will do. Natural science can't tell you what you ought to do.

That depends on what you mean by 'can'. All the information about the intentions and consequences of your actions is encoded in a total physical picture of the universe. Where else would it be? OTOH, natural science, in practice,cannot produce that answer.

It is surprising to me there is so much resistance (I mean, from many people, not just yourself) to this train of thought. When you say in that earlier comment 'You have a set of goals...', you have already, in my view, crossed out of natural science. What natural science sees is just what it is your propensity to do, and that is not the same thing as a goal.

Natural science is not limited to behaviour: it can peak inside a black box and see that a certain goal is encoded into it.even it it is not being achieved.