I have decided to give a go to few more tries and manage to efficiently make nice and clean PBR texture. I experimented with different light angles and different ambient light values during capture to get best input data to process.
Lower angle with more dramatic shadows with a bit of ambient light works better, unfortunately gradient was noticeable all the time. The only way to decrease pattern visibility was to crop really small area from input image and use few patching nodes to break it's repetitiveness.
Conclusion: Final texture size is strictly limited by initial image resolution. After cropping, not much of texture really left . In my opinion, that kind of repetitive pattern can be easily generated using Substance Designer's generators. Photogrammetry based high poly mesh also has more potential in PBR texture creation. I think I am done with that approach for material scanning and will not touch it until I find a way to keep surface lighting more consistent.
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