To reduce possible keyboard shortcut conflicts, like common X11 layout switching shortcut Alt+Shift, or various DE and WM related shortcuts, please implement the host key feature.
This is a single modifier key which client never passes to the server and uses it to trigger its own actions.
From configuration standpoint, shortcuts can be assigned relative to the host key, while host key itself is configured by separate option.
For reference, such feature is utilized by Remmina and Virtualbox Qt frontend using Control_R key by default. (They also able to distinguish left/right modifier in combinations, so you may find some clues there).
See also #1657
this ticket has been moved to: https://github.com/Xpra-org/xpra/issues/1210