IMO it won’t make a big difference, I’ve the older El-Mariachi with slightly longer stays and they’re not ‘too long’ except on paper.
Whereas my Fat Bike is too long (despite being an on-one which is quite short IIRC), you can feel the rear end/wheel pushing the bike upright as you turn into corners.
To get so short that it affects stability would take some doing on a 29er, I think on a Large sized frame the average 29er’s stays with enough clearance for sensible tyres is perfectly balanced.
If I was getting a custom frame made I think chainstay length would be minimised, but secondary to having good clearances. And there’s a lot more details I’d obsess over beyond geometry, like bottle cage mounts in unusual places for additional storage, cable guides where I want them, getting it perfectly fitted with an inline post etc. The basics of stuff like geometry I think the big brands have got pretty much nailed and they’ve had the facilities to do many prototypes, definitely better than you could make up when you’ve only got one shot at it.