Question: is there specific code to open the flies, or is that something the ECU does automatically based on something else in the tuning?
I don't think we can answer those questions, since it is something that requires disassembly of the programming. However, I am going to guess that the secondary butterflies are variable and on a map, just like everything else.
My question stems around, why would I pay nearly $400 for a single flash, when I could buy a PowerCommander or Bazzaz unit for about the same and do whatever I want?
Because with a PC:
1) It will not open the secondary butterflies, so those would still have to be removed, physically.
2) Removing the secondary butterflies cripples part of the the traction control system (but only part of it... it still still operate, just not as smoothly)
3) Restoring the bike to factory requires reinstallation of those secondary butterflies.
4) It is less reliable- There are lots of connectors and other things to install, each one having connections that can fail, be cut, go open. Plus there are more circuits to fail. And it requires power.
5) Much more labor to install.
6) There is something visible to cue possible warranty issues (the PC and the missing flies) (even that that would be bogus for anyone to complain about, it is still a very real factor).
On the flip side, the PC:
1) Gives an easy way to go back to "stock" programming (no additional reflash expense).
2) Allows for user-programmable maps and quick change of maps.
If you are a "tuner" or "racer" then you will probably want the full control and power of a PC. If you are just a regular street rider, you might prefer the simplicity, reliability, stock-ness, and refinement of the ECU reflash.