If you exhale through the bowl alot ('breath method'), all that heat and smoke will penetrate into the briar, and no amount of scrubbing will completely remove it.
Wet cleaning of the entire pipe after every smoke. Takes 3 or 4 minutes. Eliminates the need for deep cleaning. Once you get used to it, the idea of not doing it seems unpleasant.
It's the result of an overheated pipe. Very often the overheating is uneven. The main concern is that you may also be charring the inner walls of the chamber.
It sounds like you are doing it right. I had the same problem, and the only thing that completely fixed it was to change pipes. I went from a tapered bowl (rhodesian) to a non-tapered bowl (pot) and the problem was solved.
Once the seal goes, the flavor goes with it. The likelihood of of that happening increases with age. Rehydration can't do much, other than prevent the tobacco from crumbling when handled.
I tend to fold and stuff all the flakes that I smoke, even if rubbing them out might enhance the taste somewhat. Most of my pipes are on the smaller side, and it really doesn't make sense to load those with ribbon, unless you want a 15 minute smoke.