Currently, the Sculpt mesh used for projection, was duplicated as a temporary projector as you mention, but polyscript just didn't work. The temporary mesh wasn't erased even when I've pressed Escape. So I tryed again using my retopo in edit mode and selecting the temporary mesh instead of the original base mesh and it worked.
I'm not sure if I've recorded this problem.
My retopo is done and contour was super usefull but I was not really able to deal with polyscript as the base sculpt was too complexe making the bezier curves to be jaggy and really hard to handle.
To avoird projection problem, an interesting thing to is to kinda have the same workflow as polygroup in Zbrush.
You can create vertex group isolating arms, face, legs.... and assign them to a mask modifier.
Thanksfully the mask modifier doesn't simply mask the selected vertices, but it also make them to be absent in the scene avoiding any overlaping projection.... I've discovered this late, but this might be very usefull in addition of your tool.
If you're retopoing a neck, or a strong jaw and got problem to make your way between the torso and the the chin for exemple, masking the head with a current mask modifier will make your tool and anything using surface projection to work without a problem.
I'm not sure if it was super clear but... If I've recorded point of interest in the video, I'll slow down them so that you can check and will let you know the moment you have to watch without having to see a kido showing you topology... that would be really anoying for you (Topology master : )
It's not perfect but it has a really descent topology for animation, and texturing is on its way.
Whatever difficulties I've met, it tooks me about 5 hours to it I think. Wich is really descent.
I think, retopoflow usualy make me save like 30 to 60% of time to be spent on retopo.
I believe, on a smouther character it could be way more violent.... So My review won't be super accurate and I will point that.