Since the org.kde.KWin.InputDevice interface is exposed on D-Bus it is possible to alter the input device configuration. The configuration gets however reset back to defaults once the user switches virtual terminals.
Not completely unsurprising: when switching vts we lose all input devices. On gaining vt we get the device recreated.
My suggestion is that we start to store configuration when a device gets configured. When a new device is added, we check the configuration and restore the settings as in the config. This would make the changes not only persistent when doing a VT switch, but also in general (system restarts).
Implementation for the idea outlined in comment #2 at https://phabricator.kde.org/D3264
Looks like I forgot to link the bug report. Fix in http://commits.kde.org/kwin/de89176cd2a9977e4e5f6bac0bbcf2da9d1e5197