No, illegitimate debates are ones which do things such as:
- Misrepresent evidence or scientific procedures
- Fudge or cherry-pick measurements
- Exaggerate or downplay the extent or significance of discrepancies in scientific methods or findings, or disagreements between scientists
- Quote mine
- Otherwise disobey the rules and principles of basic honesty and factual accuracy.
The whole point is that science has rules. More to the point, honesty has rules. Rules that have nothing whatsoever to do with “naturalism” or “secularism” or any other weasel word ending in “ism” but that are just concerned with honesty, factual accuracy, and fitness for purpose. Rules that are the same for everyone, whether you are a Christian or an atheist, whether you are Ken Ham or Richard Dawkins, whether you are the Dalai Lama or the Pope. It is adherence to these rules that determine whether a debate is legitimate or not. Whether you or I like them or not has nothing whatsoever to do with it.
These are all at the level of fine details. None of them concern the core fundamental findings that biological populations change and diverge over time, that different species are related to each other, and that in many cases the times at which they diverged can be clearly identified.
[Correction: Common descent is one of the core fundamentals. But it is not one about which scientists hold to different views in the way that you suggest. So it does not belong on your list.]
If you re-read my response to your post, you will see that I was not talking about peer review. I was talking about a level over and above peer review: where scientific theories are put to work in situations where getting them wrong would have consequences.
Science isn’t just done in the ivory towers of academia. A lot of it gets done in the harsh realities of industry. It’s one thing to dismiss scientific findings when they’re just published in a journal. It’s a completely different matter to dismiss them when you have to apply them to situations where people’s jobs, livelihoods or even their lives depend on them working as described in the journal.