ECU Reflash - Pitfalls!?

I'm new to the whole ECU reflash world and had a few general but loaded
questions below. My purpose in asking these is twofold : one from utter
curiousity and the second being that I'm contemplating on getting a
reflash and would like to learn more....

1) What does an ECU reflash generally entail? I'm looking for some general
information on what kind of routines are changed (compared to stock) when
the chip is reflashed. I've been reading that an exige s 220 could be taken
upto about 280hp with the Gotham Tune.

2) How would a software engineer know that he/she would NOT be running
the engine/timing etc., at the very edge of mechanical capability and thus
increase the potential for future engine (catastrophic) failure?

3) I ask (2) because only with a certain number of observations and over
a decent time period can a software person know how a particular
version of a reflash would affect the car in the long run. This may not be
required if sophisticated simulation software is used but i'm presuming
that lies in the domain of car mfgs and is proprietary. Do u agree?

In general....you get a reflash, your car performs like a beast. How do
you know OR how are your comforted in knowing that the reflash is
NOT pushing your engine to its very limits/running lean and over time
there wont be higher probabilities of failure?

- aLV

PS: I'm a CS/Applied Math by training and DO understand software
engineering at an intricate level. I'm more interested here in learning how
reflashers approach this for mechanical devices such as engines etc.,