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This is a known problem and I do not have any solution. If you know how to address this please contact me.
Two workarounds:
I added the setting "nPts" under [pyqtgraph]. It changes the number of colour points the LUT gets exported with and thus the resolution of the colour scale. Playing with this value can get you closer to the image displayed by pyqtgraph or maybe even result in better images.
The residual plots have an additional problem of not respecting the symmetric colour scale for negative values and instead, matplotlib maximizes the contrast. I do not know why but one way to fix this is by opening the options window in the already opened matplotlib window (the one with lightning symbol), go to the second tab (Images, etc.) and there you can change the colour scale values. Simply choose the larger of both and overwrite the other with the same value but opposite sign, like this:
The LUT of pyqtgraph plots does not get properly exported to matplotlib resulting in different colorscales.
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