No one, I believe, directly addressed the OP's saying something about how it's common knowledge that the ride of a frame built by hand by a skilled builder is "obviously" going to be superior to that of a factory built frame, even if both were built with the same geometry, the same tubing, etc.
Coincidentally, there was a Framebuilding thread a while ago where a poster reported proposing that same point of view to a veteran framebuilder. The framebuilder replied, in short, no, that's not necessarily true. A custom builder, he went on to say, can build a frame that is closer to the ideal for a given rider, if that rider's proportions or preferences can't be easily accommodated by an off-the-shelf bike, but there's nothing inherent in hand-building a bike that makes it intrinsically superior. (The guy who had that conversation was astonished by that take and came here to ask for opinions. As I remember, everyone who weighed in here agreed with what the framebuilder had said.)
That said:
Back in the 1980s, Bicycle Guide magazine commissioned the building of seven frames with identical sizes and geometries and with seven different Columbus tube sets and had a number of cyclists ride the bikes (unlabeled except for numbers---bike 1, bike 2, etc.) and then describe their impressions of how the bikes rode.
The published results surprised me and, I would guess, most who read the article.
It's a terrific read, but for the impatient, here are a couple of salient details. Toward the end of the article, the writer says, "To be honest, I couldn't tell the difference between an Aelle frame---with straight-gauge tubing and weighing in at 4 pounds 12 ounces---and an EL-OS frame---with double-butted, oversize thin-wall Nivacrom tubing and only 4 pounds of heft." He goes on to say, "If the numbers on the bikes were switched around and I were to test each bike again, my guess is that I'd come up with different tubing preferences. I think my ride preferences were essentially random."