AFR hasn't up until very recently been used in the fuel calculation at all. Karlos' map certainly doesn't use it - i can tell by looking at the numbers. The AFR table has just functioned as a look up for closed loop. However, with the latest releases of the code, there is now an option to multiply by AFR. The idea is that this will then give an accurate representation of the engines actual VE - this is important as MS is evolving to use more model based calculations. It does however mean that with the option enabled, the table needs retuning. Not really worth doing unless you're starting from scratch.
So, before we had
pulse width = MAP x RPM x VE x delta where delta is the sum of all the various enrichment calculations (accel enrich, warm up enrich etc).
Now we have:
pulse width = MAP x RPM x VE x AFR x delta
Worth noting that multiply by MAP can be disabled in some odd ball engines where there is a lot of MAP jitter. It's not recommended though, and gives a very strange looking VE table.
Rick