I’m not sure if it’s entirely helpful, but have you tried a udev rule to make libinput ignore that specific mouse device?
We encountered something similar where we wanted/needed to to the opposite (have Wayland ignore the touch device) because we had a Qt application and needed touch2pointer for certain widgets to accept input properly.
e.g.
SUBSYSTEM=="input", KERNEL=="event[0-9]*", ENV{ID_MODEL}=="[touchscreen model]", ENV{LIBINPUT_IGNORE_DEVICE}="1"
you can identify the ID_MODEL to use with udevadm info /dev/input/eventX for the mouse entry