Hi Leon
Technically speaking, your Gemini system has calculated where the scope should be pointing, whenever you do an Additional Align, the Gemini updates it's Pointing Model and therefore makes slight adjustments to where the SCP is.
By doing what you did, an accurate Drift Align, then building a Gemini Pointing Model, you are effectively removing any major errors, the fact you hit your target each times proves that.
That is why a permanent setup is so good.
Cheers
JohnG