I think it's possible to really tune a bike based on non-fit things. I mean, okay, I have a custom frame but I have weird body proportions so I don't fit regular frames.

However during getting two frames built and then the first frame "adjusted" after learning how a particular change affected the ride of the second bike, I will say that even if I fit a stock frame I'd want to commission a custom frame to get shorter chainstays. It's incredible how much more reactive the bike acts with shorter stays.

On the first frame, when it was orange, everything seemed great about the bike. It fit well, better than anything I ever rode, and I upgraded to Cat 2 on it. The only thing that bugged me was that the rear wheel skittered around, even when coasting through a somewhat normal 90 degree turn. I had specified 40.5 cm stays because that's what the Cannondale I had prior had, but with the very long front end I ended up with very little weight on the back.

The second frame I asked for the same geometry (fit, head tube angle/length) except I asked the builder to shorten the stays to 39 cm. This would bring the rear wheel a bit more under me, allowing me to weight it more in corners. That was the length of the stays on my first race bike and although I don't remember much about it (it's been a while) I remember that it handled just fine.

When I got the bike I was absolutely amazed at the handling. The thing would let me put the bike anywhere, relatively speaking, and the rear wheel felt totally planted. I also did, immediately after building it, a number of 3-6 hour rides, and the bike was fine.

I contacted the builder and asked if it would be possible to alter the original frame from the 40.5 cm stays to 39 cm stays or "as short as possible". He agreed to alter the frame for a ridiculously small amount of money (a few race entries). He had to replace both the seat stays and chainstays as well as the brake bridge, but he sent me a naked frame with 39.3 cm stays. I had the frame painted (red, since the guy was painting his car red) and it handled exactly as I expected - super quick, super planted, super secure.

So, based on that, my thought is that even if I fit a normal frame I'd consider commissioning a frame with shorter chainstays, at least for me.