I haven't seen any issues with the gear not being tensioned, I'm not sure again what it does. The old way Honda wanted it done was to remove the whole rear cover of the engine, including the oil tank, and valve body. Then clean the oil pickup tube in the oil pan and flush everything inside the system. The way you did it (except removing the entire assembly) is the way I think they want it done now, but then again I'm not sure.
The gear inside the engine is only tensioned about 1 and 1/2 teeth. It's a double gear that has hole to line it up with a punch and then insert a 6mm bolt to hold it until you've got the clutch in, then you can release it. I've found the best way is to hoid it with the punch, so you can wiggle it a little to line the gears up. Im not 100% sure what the heck this does, but it must be something or Honda wouldn't have put it in there.
As far as the seals, you mentioned the 2 on the end of the shaft, well there are 4 larger ones on the shaft. One unit I did had a couple nicked from me putting the clutch on. This allowed oil to bleed around the clutch and not push the pistons out when reinitializing. That's why I mentioned greasing the shaft seals good before reinstalling the clutch assembly. If you look at a parts diagram on the slide labeled Transmission, you mentioned Part #1 in your post, well the seals I'm discussing are Part #2. Parts Diagram labeled Final Driven Shaft show shows the tensioned gear I'm referring to.