AE will increase the delivered fuel for an amount of time. That time is often short enough that it will not affect BLM. When you are tuning based on viewing the amount of fuel burned you will naturally be viewing a combined total. But disabling AE makes for a very challenging drive. Every time you open the throttle the engine goes lean. So the question really comes down to how do you separate the AE from the VE. I have tuned with AE disabled and the final tune was very good. But I dedicated a *lot* of time to driving and accelerating slowly to see what would happen.

AE should be tuned to cover the rapid changes that the ecm can't account for. Once the VE tables are right, a slow change in manifold pressure is no problem. But suddenly snapping the throttle open causes a massive change in pressure in a hurry so AE is used to provide additional fuel for the increase in air density. One approach is, when you have the engine operating and accelerating as you think it should be, to view the VE tables in a 3d axis. If the high load section at the end of the table seems too high or too low compared with cells nearby it suggests that the AE needs further adjustment. So shift some of the fueling toward or away from AE and rebalance the VE.