This is directly from the Factory Honda Service Manual for your bike , and yes the seal rests against the gear
The oil can transfer a few ways , from a clogged vent building up case pressure , to a failed seal , to the gasket between the 2 case halves , to the one way flapper valve on the ignition side of the case , coolant in both sides is a head or base gasket or a defective/damaged cylinder , or a water pump seal , did you also replace the Balancer Shaft Seal ?? , the right seal usually allows oil to go from the tranny side TO the engine side , not the other way , going from engine to tranny is most likely one of the things i mentioned above , i am guessing the Balancer Shaft Seal