First of all, the standard transducer for different models are different even if the technology is the same.
All units come with a transom transducer and for some models that transducer is not suitable for trolling motor mounting. The only ones that are suitable for both are the HDSI Side Imaging transducers and the MEGA SI transducers.
You should use the proper transducer for the application if you want the best results.
Humminbird's transducer exchange program consists of calling them to arrange for the exchange, send in your transducer, and they will ship when they received the transducer from you.
There may or may not be a cost difference, depends on which transducer model.
Humminbird Helix 12 CHIRP SI, 1198c SI, 1198c SI, ONIX 10 SI NT, Helix 7 CHIRP SI GPS G2, SOLIX 12 SI, 360, RC-1