So today I came back to this and decided to try an absolutely minimal configuration:
I built this in the new beta of the Tuner; installing this as a v4 .cfg file resulted in me just seeing a 'z' from either chord press instead of "command-z".
I would try upgrading to firmware 13u but this doesn't seem to be working - the light on the Twiddler flickered green and red, but when I do N+S 0R00 I get "VERSION + )>)(B".
If I pair the Twiddler to the win10 tablet that I mostly got the Twiddler to use with and do N+S )R00, I get "Version = 0.09b", and the command-z shortcut works as expected. (I'm swapping ctrl and command on that win10 tablet because I also use a spare Apple wireless keyboard with it.)
And: following a hunch, I tried pairing the Twiddler to the Mac instead of using it via the USB cable it was plugged in with... and command-Z works properly here, too.
I think I may have just uncovered a bug in 0.096b that can be generally characterized as "terrible things happen to modifier keys while connected via USB"- ctrl/gui/shift in chord definitions are ignored, and 'shift' reads as being held down for the entire duration of pressing the version string. It may or may not be a Mac-only bug; I don't have an appropriate cable to wire it to this USB3-only Win10 tablet and find out. Thanks for helping me verify that blah DOES normally work and it was something about how I had things set up!