The waypoint is marked wherever the GPS is located, so when you mark at the console, you are actually marking the console, not the transducer. Even tho you marked where you saw the cover, you will automatically be off by the distance the head unit is from the transducer. When you return to that spot, the GPS will say you are there, but you will be off by several feet because of the difference between the transducer and the head unit.
When you mark the waypoint from the bow mount and you are using a transducer at the TM, there won't be that difference because they are sitting on top of each other, but if you use a waypoint from the console at your front unit, you will be off by about 10'
Hope this makes sense