1. Stage 3 is whatever the company building the turbos decides it to be. It varies from supplier to supplier. If you're thinking of hybrids, I'd advise against it.
2. Yes, up to certain power levels. It's effectively the same box as the auto and both are good for 400'ish BHP (to remain reliable). Other people run more power through theirs and have yet to break them, but they will eventually go. The difference between the auto and tip boxes are the connectors for the speed sensors. The standard auto has one. The tip has two.
3. Tuning a VVTI car is more difficult and expensive once you pass BPU. VVTI cams are pricey, you have DBW and idling to overcome.
4. With all things being equal, the manual will cost a little more as it is easier to upgrade to big power without changing the box, and is more desirable by people that have never owned the auto/tip.
In my opinion, the flexibility you get from the tip makes it better than the auto. I had a Tip/vvti and the VVTI was more expensive and painful to tune. The torque was good though. The tip was great, but I went single turbo and then had to rip out the auto box and shove in the 6-spd which was hugely expensive and technically painful with the wiring looms.
All in all, depends on what you want.