Make sure you have xserver-xorg-input-synaptics package installed. Debian wiki could also help: perhaps you have libinput driver (which lacks some functions) installed instead of synaptics?
I’m running Qubes 3.1 on my Librem 13. The trackpad is recognized as a standard mouse, and is therefore not very functional.
The package in Dom0 is xorg-x11-drv-synpatics version 1.81,-g.fc20. I am trying to figure out how to install the xserver-xorg-input-synaptics package you mentioned above, but can’t seem to do so. I am also posting this on the Qubes Google forum, but am trying here as well.
The trackpad problems are fixed in Qubes R3.2-rc2 which I am running now. Earlier I was running Qubes R3.0 which indeed thought the trackpad was just a PS/2 mouse. So upgrade your Qubes.