This is a lamence explanation, but it will do the job.
There are tons and tons of information on tuning theory out there, if you're interested in learning it all. Buy some books & read

Air Fuel Mixture is obviously the mixture of air (oxygen) to fuel.
25-30% of air/fuel mixture energy actually becomes "work" aka thrust.
The remaining 70-75% becomes exhaust. Ignition timing & A/F ratio are both used to control the heat which an engine produces. Running a richer air fuel mixture on a boosted motor, helps absorb the heat which is produced. I.E. Charge density increases, more heat is generated etc.

Concerning enrichment safety:
In most cases the power differences between 12.5:1 and 11.8:1 air fuel mixture are usually very little. Hence, most tuners tune f/i street cars at 11.8:1-12.0:1 a/f at WOT depending on the spec of the setup i.e. compression ratio etc. Some additional factors to account for are temperature, altitude & humidity all affect air fuel ratio. Most engine management systems including Hondata do not have correction factor for different intake temperatures, altitude etc. Hence, you tune your car when its 80-90 degrees outside and target a certain a/f ratio. When it is colder outside (50-60 degrees) you can expect your air fuel ratio to change. For this reason, it is a good idea to tune very conservatively on a street setup.

Other important topics to consider is ignition timing, knock, MBT and so on.