Based on my very limited experience - I made one frame with Dave Yates - I think that the "comfort" in the ride seems to come from the forks, the rear end and the tryes and rims.
The stiffness seems to come from the main triangle.
If I was to buld the bike I have again, I'd have increased tube sizes in the main triangle and thinned down the for legs and seatstays.
My old Raleigh has noticeably thinner fork legs and seat stays and is much more compliant than my new frame.
I did a lot of research beforehand, but compromised the design because I wanted a particular style of dropout, which mandated thicker stays and fork legs. I decided against larger diameter frame tubes because I didn't like the look.
The bike is amazing to ride, but it is stiffer in the forks and stays and the chain rubs on the chainring when I get out of the saddle which suggests that the BB could have been stiffer, so a bigger downtube might have helped there.
As others have said, I'd phone the builder, ask why the bike has deviated from specification and see what they say.
The builder should have discussed this with you before changing the spec. He may have changed the spec as a result of forgetting, misunderstanding your spec, or as a result of an independent decision on his part (in which case he should have asked first).
From my perspective, I think a bigger down tube might end up being a blessing in disguise. I doubt you'd be able to tell any difference in ride quality between two bikes otherwise identical, but for the downtube diameter.