I put mine in your "other" location - just behind the mast.
It works fine except when I get in large chop, me in the rear seat and no one in the front seat, then I will get drop outs in my depth reading. I'm talking conditions where the front third to half of the boat leaves the water going over each large wave. The wife and I went out today in rough conditions to try our new dry gear out, wind was 15 - 20 kts, waves as much as 3 feet and it never missed a beat, though we may have missed a couple
I don't know how much the unit has to do with it, but its a Garmin GPSMap 441S.
Edit: I put my transducer up front for two reasons - to have it out of the way and to make the depth alarm go off as early as possible. I think the early warning is only a fraction of a second so no big deal moving it as far as that goes. I moved it to under the rear seat and carved out a spot for it in the extra floatation so it is still out of the way. This cures the losing depth reading when sailing solo in rough water.
This shot is from the center hatch looking rearward under the back seat.