I definetely do retract the gun in a wide transition.
The first two of your downsides aren't actual downsides tot he technique...you just aren't familiar with it enough yet.
It replaces 1 technique with 2, but there is a lot of stuff we have 2 techniques for. Surrender and Hands at sides draw. Reload to freestyle, weakhand, strong hand. Entering a box on an easy shot or a hard shot. Leaving the box on an easy shot or a hard shot.
With practice it will become 2nd nature just like any other technique. Just make sure you program it well during the walk through.