Here's my take on it. I have a round tubed Scandium Ocotillo w/ carbon stays. I went with the carbon stays solely based on Ves' recommendation, having told me that they would be stiffer than alu. I don't believe comfort ever came into the equation when making that particular decision.
Now here's the thing: As a few other people have pointed out, I don't have an otherwise identical bike to do side-by-side comparisons. And even if I did, those "tests" would be purely subjective and not worth beans to the scientific proof crowd (yes, I miss Andy Coggan).
BUT...
Why did I buy a Yaqui over a QR or a Cervelo or a TitanFlex? I bought it because of Ves' wealth experience in building triathlon bicycles. I bought it because I trust his opinion and judgement, and wanted his expertise. Why then would I not go with something he specifically recommended?
You have a unique "problem" in that you are purchasing two bicycles at once - so a $400 upgrade is really likely to be an $800 upgrade. Suddenly the money involved is a little more significant. Be that as it may, how easy is it to drop $400 at a given point in the future for a new set of bars, or cranks, a wheel, or an aero fork? Those are all upgrades that can be made at any time. Having carbon stays is an upgrade that can only be purchased prior to the bike being built.
If I were in your shoes, I would take Ves' advice and purchase the carbon stays. This is not to say that if you opt for alu stays you will not love your bike - but you will have deliberately strayed from the optimal path set before you by the man whom you have entrusted to design and build your bike. Effectively, you will have (in a small way) sabotaged your "perfect dream bike" in a manner that cannot be later remedied without starting over with a new frame.
<If you're gonna be dumb, you gotta be tough>
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