Based on the fact that the area to the inside of the transom is open and below where you are talking about, I would guess it makes no difference, unless there is separation between the two places internally.
However more importantly,the battery is placed by there! so if water comes in, that isn't good. Either get the battery inside a plastic battery box with strap over, or move it under the console/seat etc. Having it open in an area where water is, will only end up one way!