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Hi Goofy,
thanks for your very generous answer.
At first, yes you are right the thin wall problematic is the main problem with scaling.

I did not mean exact your STL file. I meant the STL Format itself where holes were discribed as a function out of triangeles. I think big holes like the thread in 12mm are not problematical but holes with diameter of 2, 3 or 4 mm are mostly much smaller as in the design.
In the internet there are tables available where for a defined real diameter a diameter is given for how you have to design the hole in CAD to reached the defined diameter.

But your are definitly right and I am on your side if you say in CAD you design the part in a perfect fit and compensate in the slicer if neccesary. That is a good approche because the 3D model should be perfect without any compensation because then you can mill it out of metal or other materials.