StateMachine States in SignalTAP

Quartus defaults to one-hot encoding as long as it recognizes the state machine and there are more than two states, so it should not be hard to get it to do that. Maybe search your .qsf file for any settings that affect state machine encoding and remove them (that can sometimes be easier that finding settings in Quartus).

As for SignalTap, when you use the node finder to add signals do you use post-fitting or pre-synthesis. I recommend pre-synthesis because the signals match your rtl code and state machines should be listed as one-hot with the state names matching the names you defined in your rtl.