I haven't test Tinfoil with the Trinket desoldered but I believe the issue is purely software. It seems to happen if I use certain install paths on the PC (e.g. if I define the path as relative it will crash, but not if I define it as absolute).
My issue with the volume button hasn't gone away but it's definitely a hardware issue. I've measured the voltage on the Up button and it does go fairly low without being pressed, around 0.5v or 0.3v sometimes, while the Down button is always 1.8v. So the Up button isn't shorted to ground but it's defective somehow.
My guess is that the Tegra uses an internal 1.8v pullup on both volume buttons and the Up button pullup is broken. I can only assume this is because of the Trinket; I had the Trinket connected to the button at some point before I finished the install. It probably pulled the button input high to 3.3V while in bootloader mode or something, and I'm guessing the input is not 3.3v tolerant, so it broke. It sucks but I will try putting an external 1.8v pullup on it and hope it works.