Well, this is certainly strange!
This may be overkill, but the fastest way to reproduce the issue is probably to run QubesOS in a virtual machine (I believe VMware has prebuilt ones if you don’t already have one).
Open a Debian-10 or Fedora-32 Qube, and run the corresponding setup command:
Debian: sudo apt update && sudo apt upgrade && sudo apt install python3-pip python3-tk libusb-1.0-0-dev libudev-dev -y && pip3 install onlykey-agent --user && wget https://raw.githubusercontent.com/trustcrypto/trustcrypto.github.io/master/49-onlykey.rules && sudo cp 49-onlykey.rules /etc/udev/rules.d/ && sudo udevadm control --reload-rules && sudo udevadm trigger && export PATH=$PATH:/home/user/.local/bin
Fedora: sudo dnf install python3-pip python3-devel python3-tkinter libusb-devel libudev-devel gcc redhat-rpm-config -y && pip3 install onlykey-agent --user && wget https://raw.githubusercontent.com/trustcrypto/trustcrypto.github.io/master/49-onlykey.rules && sudo cp 49-onlykey.rules /etc/udev/rules.d/ && sudo udevadm control --reload-rules && sudo udevadm trigger
These both reliably create an environment to replicate the issue (both in Standalone and Disposable Qubes). The issue doesn’t seem to be Qubes specific, since aside from using stored keys everything works as intended.