Putting the motor in the frame will upset your center of gravity, but it's only a moped, so probably won't matter much.
Pedals will be useless, because they'll be up really high, and may hit the tank (or your chin.)
You'll have to get the chain line right.
Exhaust comes straight out the bottom, which might be obstructed by the frame.
you have to make sure there's enough room for the carb on top.
And still need the swing arm, so cutting off the motor mounts will leave a big empty space underneath.
But it could be done, just needs a lot of work.