Modern GPS receivers are sensitive enough to work inside a GRP boat (unless you put them directly below some metal fittings), but they'll perform worse than one mounted outside. Also, the location is often closer to the mast, boom and stays, which block a clear view of the sky, so you get fewer satellites at good angles and thus a less precise location (which is usually fine too).
So if you want the perfect signal, inside isn't great. But it'll probably be sufficient, especially if the GPS signal is only used for AIS, not plotting your own location on your chart, for which you probably already have a better situated GPS receiver. Doesn't matter if the ship sees your boat 5m away from its actual location as long as it sees your boat. You can always wire it up temporarily and see how the reception is before mounting it there.
Oh, and do check the mounting instructions for orientation. Upside down mounts aren't always going to work depending on where the GPS antenna is inside the unit.
