How to choose the RMS setting when calculating the amplitude？

Look, there's no such thing as a 'real' result! All dB measurements are relative ones, and all you have done is changed the reference value. Normally the reference would be 0dB FS with a sine wave value, not a aquare wave. The reason for this choice being there is historical, and not relevant to what you are trying to do.

And I think that you are only disturbed by the choice because you haven't grasped the fundamentals yet - quite. Persevere!

This has nothing to do with the crest factor. If you define a signal that reaches 0dB to indicate 0dB if it's a sine wave, then that's exactly what it does. If you substitute it with a square wave, then the RMS value will be indicated as 3.1dB. That's +3.1dB. In other words, 3.1dB higher than the sine wave RMS value. This is correct. Now if you change the reference to use a square wave instead, both values will be 3dB lower. So that's 0dB for the square wave, and -3.1dB for the sine wave.

If you want to see all this laid out clearly, look here: Wikipedia - crest factor