I have a WindPaddle Adventure sail and use it with my Outback. I don't have the Hobie sail kit, but based on my experience...
With the Hobie sail in place it would be impossible to stow the WindPaddle sail in the normal way. To work with a pedal drive boat, they sell a "shuttle kit" which is just a spreader bar that mounts to a Ram ball mount that goes in the sail mast hole and a couple lines that run back to the seat mounting padeyes. You clip the sail to the lines and let it unfold into shape, then push (or the wind drags) it forward past the pedal drives. With the Hobie mast in place you'd have to leave it in front of the mast - or actually climb forward and mount/unmount it up there.
I don't think you'd be able to unmount it while under way anyway (without modifications) since the sheet is a continuous loop tied to either side of the fiberglass batten and would thus be on either side of the Hobie sail. You'd have to untie one side or leave it looped around the Hobie sail when folded up. While under way, I imagine the downwind side of the Windpaddle sheet would also be in the way of the Hobie sail too, I don't think there'd be enough room under the Hobie sail for it.
Yes, it depowers instantly when you let go of the sheet - because the wind flips the top forward so it winds up laying flat on the kayak. That works fine for a standard kayak, but is a real problem on my Outback. Normally the sail is immediately in front of you at the front edge of the cockpit coaming, so there's plenty of kayak for the sail to lay on. With the Outback (and possibly other Hobies) the sail is much farther forward to be out of the way of the pedal drive. When the sail lays down flat there isn't enough kayak left forward. The top of the sail drops over the front of the kayak - and if I'm moving with any speed at all it almost immediately grabs water and becomes a highly effective drogue chute! It's also a real pain getting it back when this happens.
And finally, the reason the Windpaddle sail can handle so much higher winds is because it takes a lot of wind to get it to go anywhere in the first place. When I try using mine in lighter winds it just doesn't do much - a very light pedaling produces more speed. It will finally get my Outback to 4 MPH or so when the wind is up around 25 MPH! It does work on a broad reach, but the speed drops off dramatically the farther off wind I go. It's best straight downwind.
Not to disparage the WindPaddle sail, I quite like it and it's a very compact and convenient way to put a sail up on any of my kayaks on a windy day. I just don't see there being a feasible way to use it with the Hobie mainsail. By the time you've modded things to make it workable and safe, I think you might as well do a standard jib or spinnaker.
(In my opinion. I'm not a sailing expert by any stretch of the imagination. YMMV...
One more thought: Unless you mounted it well in front of the Hobie mast, I'd think you would lose a fair portion of its sail area? Since it's centered about the Hobie mast, half of it would be shadowed by the Hobie sail at pretty much any point of sail?