Yes its the inch or so at the nd that does the receiving, so the radio can go anywhere convenient letting the aerial go where needed.
The active bit of the aerial needs to be above the waterline, it should be remembered that anything that can conduct electricity will, if in line of sight between transmitter and receiver, block the signal. Dry wood and plastic, OK. Metal, soaking wood (shouldn't happen, but still....), carbon fibre, metal plated plastic, all of these can block the signal.
Single aerials don't care which way they point. Twin ones do say in the instrucions that the two elements should be at 90 degrees to each other, but it doesn't matter whether thats vertical or horizontal or anything between.
Old style long aerials were difficult to block, the relatively tiny 2G4 aerials can be accidentally blocked much more easily.