They do scan tickets on our thruway bus (at least, the last time I took one, pre-pandemic). Not sure if they transmit any data contemporaneously, though, our driver said it's for reimbursement from Amtrak. The thruway bus I take between Bend and Chemult is operated by a contractor, not by Amtrak.
That said, Hubby and I once did exactly what you are proposing. Ten to fifteen years ago, we got a lift with friends from Phoenix to Flagstaff for a westbound SWC. This allowed us to spend time (and go out to dinner) with our local friends. There was no problem getting on the train, but while waiting in the station one of the people that had taken that AmBus said their departure had been delayed while they waited for some people who never showed up. Oops! I did not confess that we were the ones who caused the snafu.
After that experience, I'd get my tickets changed next time, at least a note attached to the reservation that we wouldn't be on the bus. You never know if the driver now has a connected scanner, or if s/he will know you are on the manifest and therefore wait for you till it's almost too late.