All these questions are answered in the article.
a) It is possible to get the data out of the stock ECU. The TECHTOMS company had that ability till Toyota shut them down. If you look on their site they offer no Toyota ECU tuning solution after 97. They only had the ability to read the data not alter it. So they dumped what they could use into the daughterboard and added their own code to get it to operate like a normal multi-map ECU.
b) The TECHTOMS writer offers live mapping, but no longer supports Toyota.
c) As for copying. I have seen tuners able to copy Honda chips, like Spoon and Mugen. Its a simple matter of taking the EPROM off the board, putting it in a reader, uploading the data, and burning it back to the new chip. And I know people who've done this for their Evolutions and older WRXs. My friend had a MadDog ECU for his Evo III and it had a board which had switchable chips on it. Those chips seem to have a lower form of protection. I've opened many Honda/Mitsubishi/Nissan aftermarket ECUs and they seem, for whatever reason to have very little protection. This is in stark contrast to the 4E and 4A ECUs I've seen. Those tend to have physical and electronic security. My blitz still has its security stickers on it, but i've seen where people open their ECU only to tear the board off the main one because it was glued to the top of the box.
As a Link agent i must admit Link usually do the same, but if something is created then it can be reversed, always!
I'm sure it can be reversed but... 1) Toyota owns the company that makes its own ECUs, so unless someone inside the company releases/steals the protocols/software/hardware to emulate a Toyota ECU only TRD and TOM's will have the capacity to do. 2) TECHTOMS already did this, because I'm sure they got no help from Toyota, but this requires using Toyota's copyrighted source code and that will get you into trouble should you start offering something commercially. I suspect part of having their ECUs work differently is the reason they have a better intellectual property claim over the traditional cell/fuel/look-up system the others are using. 3)Is there enough of a market to warrant the resources needed to crack the stock ECU when other solutions do fine.