#1 True
#2 None of the above, the 12 minute tune wipes the short and long term fuel trims so the bike can relearn them with the new set up. It does not necessarily resolve anything.
#3 Both. With a PCIII you can go to any Dynojet tuner and get a custom fuel map. With a Tuneboy, good luck finding someone. There are plenty of Tuneboy tunes out there to get you in the ball park though. The Tuneboy site is a good place to start, then the Trading Tunes section here.
With the Tuneboy you can open the secondaries 100% of the time, advance timing in 1st and 2nd gears, correct the speedo, change the rev limiter, run diagnostics and so forth.
Keep in mind it is helpful to have a lap top or a computer close to your bike with Tuneboy. You are buying a license and a cable. You can down load the software and tunes for free now from their site and play with it on your computer.
http://www.tuneboy.com.au/index.htm
Go spend some time in the trading tunes section and see what you think. There is some good discussion there.