Woodsman,
I can't remember if it was bateau.com, or Glen-L Marine designs or where, probably both, but I have seen the same question asked. The answer from the experts was yes, you can raise the prop but remember when you cut a tunnel, the entire hull will ride a little lower at that point.
In high power applications, the design of the tunnel helps force water to the raised prop or impeller so it works pretty good.
In your case, using an electric trolling motor, the water isn't going to be forced through the "chute" of the tunnel to the prop. It still might get your motor up some, but I think you'd be splitting the difference with draft.
What many flats boat designers do to make up for the draft lost in the tunnel, is to add sponsons behind the boat to keep the draft numbers low. The sponosons add the flotation lost to the tunnel.
I have drawn and dreamed about using bow thrusters, impeller fitted electric trolling motors on each side and all sorts of whacy gizmo daydream small craft low draft powering ideas. So far, every time I research them out, somebody has already tried them or there are other issues that pop up as to why no one uses it. Weight, fuel, battery consumption, thrust efficiency etc.
As far as cutting edge design on getting a boat to float shallow, you might peruse the East Cape Canoe site. Here's a picture of their Caimen model, with the sponsons.

Their website is
http://www.eastcapecanoes.com/index.php I haven't been there in quite a while so I'm not sure what's still going on but it looks good when I just stopped to get this picture for you.
Those guys build really pricey boats. They are nice. I think they know shallow pretty good.