The 300 or so RPM difference between lockup and non-lockup is probably well within the amount the ECM can compensate for the expected vs. actual load on the engine.
That'd be my take anyways. The difference in load between auto and manual is the torque converter. Although GM installed tens (probably hundreds) of different spec torque converters in the trucks, none but MAYBE diesel are so different from each other that the ECM can't easily compensate for the different characteristics.
Timing (and I'm sure base fuel, so remember, fueling isn't using O2 when the engine is cold) is quite a bit different between manual and automatic PROM's. Although timing is also "fluid" to a degree with EFI, if the engine starts to knock, EFI takes timing out, which would really hurt in an emissions test.
Probably overanalyzing this, but the ramifications to the system are quite large when making even minor changes, whether the ECM is able to compensate or not. Since this is going to be tested via emissions, you are going to want it running as optimally as possible.