How should you calibrate your print for right dimensions? My way and a question at the end

Hello,

in the last couple of weeks I red a lot about the calibration of my printer so it will produce the most accurate prints I demand from it. Most important it should produce prints that fit, are the right size and also fit the screws that should go through them. This here is kind of the way I took the last couple of days and summarize a little what I learned, but in the end I got a question that I can't really solve. I would greatly appreciate your feedback, thank you.

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What have I learned?

1. Ditch the eStep calibration you have done with the calibration cube. You are not supposed to stretch the print in different sizes. It is important, that you measure the movement of the axis, not the print! For example you shrink the print. This means you compensate your overextrusion on the outer dimensions, but what about the holes? They were smaller because of the overextrusion and the even get smaller because of the shrinking though the eStep change. (Hopefully I explained this good enough)
2. Calculate your eSteps, I used this calculator for it. This will give you the movement the printer makes and not the dimensions of your print! Because the dimensions of the print are affected by multiple other settings which we will se in the following.
3. Check if your print head really moves the amount you tell it to. I used some tape, a pen and my caliper to measure the distance the head moved as precise as possible. So tell the printer to move 100mm and check if it did. With the default setting, my printer was nearly on point (tenth of a millimeter of or so)
4. Calibrate your extruder! This is the crucial part. This is a big step because other people have made good tutorials for it. I used this tutorial by MEH4d on thingiverse (Tip for Cura users: Look for Flow (Extrusion multiplier), Line Width (Extrusion Width)). The thin wall test was good for me at 95% flow rate. For the s-plug I used the horizontal expansion setting at -0.15 but I am not really satisfied with this setting, because I don't really understand what it does to outer and innner perimeters.

So this is how I calibrated my extruder/printer. Feel free to leave me any feedback as I would like to learn more about it.

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So my question: As you are not supposed to change the eStep values for the x, y and z axis, how am I supposed to compensate for a slight error in my calibration cube? I printed one after all the calibration above and following data I measured with my caliper:

X-Error: +0.1mm (So cube was 20.1mm)

Y-Error: -0.2mm (So cube was only 19.8mm)

Z-Error: 0.0mm

If both were too big I can work with that and maybe go bag to "overextrusion", but how am I supposed to calibrate anything if there is a negative in one and a positive in the other axis?

I would love to here your advice on this, thank you very much!

Also: Please correct me if I am wrong somewhere because I am still learning about this topic.