Here are a few other observations on my part, some of which I surmise rather than have hard evidence for:
I was just about to answer the point which PN made, concerning the answering pennant at the 'dip.' I would think this procedure made the whole process quicker, especially if there were a succession of hoists to be answered, rather than having to hoist the flag all the way from the deck each time.
In the case of the repeating frigate, although I don't know for certain, I would imagine that if the flagship was expecting a reply from all the ships in the fleet, the frigate would wait until all the ships had hoisted their answering pennants and then she would signal the same to the flagship. So conversely, the signal officer in the flagship would have his telescope trained on the repeating frigate.
I don't know if anyone can confirm this, but I have an idea that signal flags and command flags were broken out at the masthead, or wherever, rather than being hoisted loose: a) because so doing would make more of an impact on the observer; b) the flags were kept tidily rolled in the flag locker in any case (and I can remember rolling the union flag like this when in the scouts, when a sharp tug would loosen the turn of the tack rope around it); c) hoisting flags rolled would prevent them getting less easily fouled by some part of the rigging, on their passage up the mast. I think, however, ensigns were hoisted loose.
It might be worth bearing in mind that the trucks on the top of the masts were usually fitted with two sets of halliards, one each side of the mast and so making successions of hoists on the same mast easier.
Incidentally, I think you'll find that the Trafalgar signal was made in a succession of 12 hoists, and I think from the mizzen mast. The way the signal is hoisted on the Victory today is, of course, historically incorrect.
Visiability of course was important when sails were set, and I would imagine that upper ones, such as royals, might have been temporarily taken in to enable flags to be seen more easily.
All of which doesn't really help Tony with his specific questions
