Let me be more clear:
When gearing up, 1)first clip on 50% bottle. Bottle tail is clipped on left d-ring above SPG. 2) Second, move 50% bottle up, slide stage underneath and clip off above SPG on hip also. Stage as used will help lift 50% bottle up and makes for nicer travelling.
3) Clip 02 on leash, clip leash under SPG on hip.
When you do bottom stage switch to back gas, no big deal and simply stow stage. Next switch to 70 bottle is easy as it is the bottle on top and easiest to access for the gas switch.
Then unclip stage tail with left hand. Confirm you have unclipped bottom stage and not 50% bottle by moving it back and forth. Using same left hand, unclip leash which is easy to find as it is on the bottom. Bring 02 forward by holding leash in left hand and unclip nose of bottom stage with right hand. While not letting go of leash with left hand, clip bottom stage nose to leash, then unclip 02 nose from leash. With left hand still holding onto leash, and right hand on nose clip of bottom stage, slide 02 bottle under 50% bottle that you are breathing and clip nose of 02 bottle to left chest d ring. With left hand (still holding on to leash which now has empty bottom stage, clip leash on to bottom of left hip d ring. Finally, clip tail of 02 bottle to left hip d ring above SPG.
This sequence is very methodical and is what we practise on 3 bottle drills all the time. Also what we just did for 2 weeks in the Red Sea with AG. You can also do it on a scooter without letting go of the trigger but there is a bit more drama attached and I tended to stop for a few seconds for a part of that move.........

I did film AG doing the whole thing on the trigger.
If you don't believe that your SPG will be trapped if you don't put the leash under it, try it for yourself. It is a pain in the ass, but yes, you can maneuver the SPG free. Not a problem I want to have if I can avoid it and I can so why bother.
Cave people may do this differently, but I am not a cave diver so I know zero about that. As far as the leashed bottle being in the way, you don't even know it is there if it is clipped correctly. It is out of the scooters prop wash and behind the plane of your shoulders and a non event.
I forgot one thing: It is very important that the leash always be in the left hand and you do not switch hands. Every time you switch hands you run the risk of losing your bottle and since you 02 40 is probably buoyant, and your bottom stage definitely is, they will both dissappear very quickly. Not switching hands is super important and is one thing people tend to do and that you will get beat up on if someone sees you do ........someone with blue gloves for example........