On my old tinnie I had anything up to three transducers mounted side by side - one pressing between each - screwed to a piece of starboard that was bolted to the back of the boat. In theory you will only ever use the front unit when you are actually fishing and as such you can get away with a "less than perfect" install for the transducer as it will never have to work at speed. I had the transducers on the port side - a stand alone sounder and a combo on the console and another stand alone sounder up front near the electric.
If you mount the transducer on the motor, it will turn with the motor. As such if you have the motor taking the bow to starboard at 90 degrees, the image shown on the "port side" of the sidescan display will actually be directly in front of the boat. If you are on spot lock and the motor turns to face the transom - left is right and vice versa.
When you mount the transducer on the motor, from memory you had one of two options. The cable can either be run in the groove on the shaft secured top and bottom - to do this the cable has to be small enough to fit and the plug had to be cut off to pass the cable through - warranty void instantly and still requires a heap of slack for tilting/stowing. The second was to secure the cable at the top and bottom but you had to leave enough slack to go around the mount and to allow the unit to be tilted/stowed. You can only secure the cable top and bottom so the motor depth can be adjusted as required and the motor stowed. With either method you have to keep an eye on things to make sure the cable doesn't get wound up too much as the motor goes about it's business, tangled with the motors cable or the slack caught up in other things (namely your feet).
There will be no difference in the reading on the sounder itself. I just personally could not be stuffed having to worry about cable management - I go fishing to relax and have a good time. If you were a hard core tournament fisho it may be worth the hassle to gain the length of the boat in time as you travel forward but in my mind that would be the only reason.