What is meant by the term "baseline noise" in this context?
I would interpret baseline noise to be the RMS noise around the baseline, under what conditions we do not know. Baseline usually implies that the signal is around a 'relative' average value. Because the RMS measurement does not care about mean values, and only the noise is being measured, it doesn't matter what the offset in the system being measured. 

I assume that the inputs would be shorted, because that would give the best results for a noise floor measurment.