The wing nut goes below the boom because:
1. It is the only way you can operate it and it does not foul or damage the sail.
2. The reefing procedure on a Wayfarer calls for the boom to go up. We first take in the reefing line before we lower the sail, That is to avoid the boom dropping in the cockpit which would prevent sailing.
3. If the boom can touch the transom as you write, there is enough play for the kicker.
4. For bridge shooting it can be a blessing if the goose neck allows the boom to go all the way up against the mast. On my modern mast I have to take the boom off the goose neck before lowering the mast.
For racers the height of the boom on the mast is fixed according to the class rules, yet many cruisers prefer an adjustable goose neck for these reasons:
1. When pulled down it gives an effect similar to pulling a Cunningham hole down, though mathematics tell us it is not the same thing. I would prefer a real Cunningham hole.
2. Lifting the boom is used for some types of boom tents. It gives a little more head room.
3. It makes hoisting the sails easier. Specially old sails where the luff cord has shrunk. The goose neck is lowered after the main has gone all the way up. With a fixed goose neck the boom has to be put on the goose neck after hoisting the main. The latter is more complicated.
It makes sense to add the (for racers mandatory) black bands to the mast. They allow you to set the boom at the correct height for sailing. Sail makers cut their sails to the distance between the black bands. The class rules tell you where to put the black bands. I have added an Aluminium strip over the sail groove at the upper black band. This stops the sail at the top. A very helpful thing since you cannot see if the sail is at the upper black band from within the cockpit. Please note that all masts are longer then required and the excess length above the upper black band varies from mast to mast.