The ECU must add or subtract fuel (short term fuel trim/injector pulse width) to maintain an AFR of 14.7 at all times until you pass some threshold and go into open loop.

If your motor is modded and flowing more air, then the ECU will add fuel to keep a 14.7 AFR. After a while the ECU will apply these corrections to an average, long term fuel trim.

I'm sure you are right about the WOT AFRs being effected by the injectors but I think nailing down the LTFTs will make the WOT tuning much easier, with less change due to temp/environment.