That train is not operated by SBB, but by Zentralbahn. Basically, seat reservations are managed by the operator in the first place. (Zentralbahn are just using the Lucerne Tourism webshop instead of running their own.)
Booking reservations of other operators via SBB is a rather new development. It may not work, as you obviously just found out. Or if it works, the user interface may be very limited or rudimentary compared to the ‘original’, such as seats assigned for you vs. being able to select your seat yourself.
