My understanding was more that the machine was not reliable and he basically had to piece the piece together / so each shot was the perfect run of potentially a number of attempts
He mentioned two main problems, the marbles would get jammed and the timing was off so the beat wasn't very tight. Both of those things should be fixed, or at least greatly improved, in the next version.
This has been his "problem" for almost a decade. He's trying to build something that's midi-tight. As a musician, somehow he forgets that real musicians also lost the beat now and then, and it makes the music more interesting.
The number of times he's postulated that some design would fix these problems is too damn high.
Professional musicians don't really "lose" the beat. A pro drummer stays on beat, while making small, predictable variations to the timing and the sound that make the music more interesting. That's not the original marble machine though, which played like a sloppy beginner.
I'm pretty sure he understand how all this works because I've heard him explain it before. If at some point he thought he could achieve precise timing down to the millisecond, I must have missed those videos, cause he seems to understand now that's not realistic.