There are certainly ways that a trolling motor could be utilized as a stern thruster on a C Dory, but in reality, especially with twins, it is just not necessary. Prop walk will work well. (Now just get the counter rotating lower hp outboards--maybe adapt the lower units of larger motors?
One of the major problems with any tunnel in the hull is turbulence. In the bow, you will notice all sorts of dips and bumps to minimize this effect. If you put a tunnel in the stern, even with 26 degree dead rise, the turbulence would kill any outboard efficiency.--and most likely make the boat unmanageable at planing speeds. The reason they are put on the flat of the transom on inboards, is to get away form any running turbulence at semi displacement speeds on up.
There are several "pod" type of bow thrusters, which might work for the C Dory--in fact, I believe that some one did put one in. Again, this is really overkill, but if you have a lot of money, and don't want to trailer, it will work.
Note that the last graphic does show a stern thruster mounted on the swim step of an I /O. It will be in a turbulent area, but will still give some increased drag. It is aft of the I/O unit--and would work as a thruster in this case.
There are also bow deck mounted thrusters...but that has its whole set of issues, with mounting and deck space. I have an 83# thrust trolling motor on the Caracal--works well on the cat because of almost square profile, and lays on the gunnel forward[/url]
I am sure that the jet type of Thruster, has improved, but I delivered a Morgan 62 a number of years ago, with the 2" jet type of thrusters, and they were almost worthless.
One of the smallest stern thrusters, is the modified Lewmar 2 hp bow thruster (about $1800, with stern thruster kit, $1300 without). It has a tunnel diameter of 140mm. about 5.5". This is pretty good size stuck under a swim platform. Lewmar makes a 110 mm (4.3"), but no conversion kit--possible, that could be used, but so many issues keeping the motor dry! A trolling motor or pod would be much better.