I think its unlikely that the market size warrants a custom version of Axoloti for guitar/stomp box users, especially as the existing one is so easy to adapt - though there is nothing stopping someone trying to build/sell one if they believe otherwise
as others have stated, depending upon how much effort/time/skill you want to put in there are different approaches -
axo not a big board, so will easily fit in, then
- with some diy, you can add pots/switches,
- or alternatively use midi...
- bypass, you could use a wire up a true bypass, but I've also supplied an object which bypasses the adc/dac in software, that may be enough.
the only thing you need to really consider is powering, for this, you will probably want to keep the 'midi din' section, as this also contains the dc power, but you can disconnect this part of the board, and reconnect it, if the length of the axo board presents an issue for your case.
so depending on your needs, using an existing axo board in a stomp box enclosure might be no more than drilling a couple of holes for the audio io and usb host.
but with a little simple soldering you can really customise it to your needs, with pots/switches etc.
@Gavin raises interesting points, because Axoloti can do some many things, you might want lots of switches/pots to try to capture lots of different uses.
but I think its also valid to take a minimalist approach, use only (e.g) 4 pots on, and then let that drive what you can do and your 'user interface' - this will make you 'creative' in your patch creation e.g. a 'character' knob might change many different parameters in your patch, rather than having lots of knobs controlling individual parameters.
(if you look at commercial products this is pretty common, partly out of cost, but also for end user usability)
I've been struggling with this myself recently, because Axoloti is so open, its easy to get paralysised by choice (''the paradox of choice'), sometimes its just better to create restrictions/boundaries, so you can then work within them!
(nice thing about diy is, even if you choose 4 pots, nothing stopping you later adding more.. and Axoloti is relatively inexpensive, so could also build multiple pedals)