I wouldn't expect you to pull the pin when you douse the main... all the slugs will fall out and, as you said, you'll have to feed them in again. Pulling the pin is only required/suggested for when you need to get the reef tack down to the gooseneck. It would be real nice if that pin was closer down, but it is what it is.
If the reefed sail is bothersome, then yes, leave the ties in place but please don't use then for any purpose other than to loosely gather the reef fold. I've seen more sails torn when newbies tightly tie all those tight around the boom before hoisting, only to tear a couple when the hoist the sail, or when it first fills.
AS for your cunningham/reef tack situation.. maybe buy a tack hook for easier transfer... you'll lose a bit of purchase but also a lot of friction, so it may be a saw-off. Then it's a simple matter of moving the hook from cunningham cringle to reef cringle as required.
1984 Fast/Nicholson 345 "FastForward"
".. there is much you could do at sea with common sense.. and very little you could do without it.."
Capt G E Ericson (from "The Cruel Sea" by Nicholas Monsarrat)