This probably doesn't help at all. Quoted form Chapman's 'bible' of seamanship.
The U.S. ensign is proper for all U.S. yachts, without reservation. This is "Old Glory," with 50 stars and 13 stripes. All boats, when at anchor, fly it from the stern staff, if so equipped, only while occupied. It is flown from the stern staff of powerboats underway on inland waters. If the powerboat has a mast and gaff, the proper display is at the gaff. On a sports fisherman, where a stern staff would be in the way of the action, the practice is to fly the ensign from a halyard rigged just behind the tuna tower.
I agree that the stern of the boat is appropriate for a smaller pleasure power boat but unless you are in a parade or regatta, if will get in the way when fishing.
I am not a big fan of flags mounted in antennas on the hardtop or a gunnel but a lot of folks do that. The larger the flag, more stress placed on the antenna. There are mast poles available that are stronger that can be mounted on the hardtop as long as the area you mount it is ranforced for the load.