You can use it through the seat scupper but you would need to remove the little cap that threads on the wire - once that is gone it will fit (Lowrance has already confirmed that the small part can be removed without issue)
You would probably need to come up with a new lower profile washer or cap of some sort - that standard Lowrance cap would seem to be in the way in the seat area - but I haven't tried one to see if it hit me or not.
By "the little cap that threads on the wire" I assume you mean the scupper cap. I did remove that, but the transducer will not fit through that hole unless you either:
1. Ream out the hole and thereby lose the threads. or
2. Take off the nut that holds the connector to the actual unit on the other end from the transducer, which would enable that end to get through the seat scupper hole as is, but you would lose the nut that holds the connector to the screen, which is the route LazyLefty went, apparently with no real problem. I'm more tempted to try this way than reaming out the threads...