My 05’ scion xa has always had a problem with vibration and some vibration sounds when stopped at a light or parked but both go away when i put the vehicle in neutral. It got so bad at one point the seats would shake, i took it to toyota and they replaced all the engine mounts. The vibration isn’t as bad but very noticeable. Could it be the A/C? The problem exists with or w/out the A/C on including the heat.
U should go to dealer/used car lot and drive another similar car? See if that car shakes as well?
Have the plugs and wires been changed. How about the MAF IAC sensor cleaned?