The stock switch controllers are probably a bit small, the only saving grace to them is that you can rest your middle, third and pinky finger on the back to be a bit more comfortable. That was my immediate hand position they gravitated towards when I tested this. Additionally, you could print grips that attach to the JoyCons that give them a more deck-like profile(Nintendo Joycon Split Comfort Grips by Tron08 - Thingiverse or Joycon Grips by user98765 - Thingiverse). Additionally, third party controllers like Nyxi and Binbok appear to be far more ergonomic for less, even when they have hall effect sensors in the sticks. I know people use those and love them with the OXP2, so they should be a solid contender.
I just don’t really get the bad rap that JoyCons have. There’s plenty of ergonomic options, they’re inexpensive and available, and it removes the need for designing a PCB, weird adapter boards to convert other controllers or other general MacGuyvering that would be needed to make an integrated controller for a design like this.
As I don’t have a Framework main board I missed out on their dev board program I guess), the best I have is a fully printed prototype, with fully modeled main board and battery inside to check clearances, fit and finish. I do know the general concept of Joycons and an external touch display works as per PitstopTech’s video linked in the OP, so using a similar setup with proper fitment of the components, I don’t see why it wouldn’t work.