I have a Helix 10 gen2 Mega Si. The transducer is mounted on the stern of the boat but it is a 17 foot stick steer boat with the console at the front seat. I have an iPilot enabled terror 55 on the front that is networked to the Helix. When I want to run a 4 foot contour with the autopilot does the sonar adjust for the fact that the transducer if 17 feet behind the trolling motor or is there a way to adjust the offset of the system so that the front of the boat is kept at 4 feet? (obviously with a 17 foot boat it is theoretically possible for the stern of the boat to be in 4 feet of water and the bow to be nearly on the bank). Haven't been able to find anything on this topic so any thoughts are appreciated!

No there is no transducer location offset. GPS/Mapping is the GPS antenna location (internal GPS antenna).
The 4' map contour is GPS based not sonar based so the transducer on the transom is not involved in that function.

thank you. Does that include when you are making a map? (I am on a private lake without a hummingbird base map)

Most definitely you want GPS and sonar at the same location when doing mapping so the contour lines will be where the actual depths are.

If you are collecting data were depth is changing, you want the contour lines to indicate the depths as they change where they change. A 17' error is useless.

I hear ya, hence my original question, is there a way to set the offset to 17' so I can correct the difference given I have my GPS on the bow and my transducer on the stern?

Alternatively, should I install a thru hull transducer in the sam location as my display unit?

Just mount an external GPS puck on the transom or the other option would be to put a transducer on the trolling motor and leave the trolling motor deployed. You should be able to run about 10 mph with the troller deployed while using big motor.