Even though the issue seems to be caused by the MasterFlat, this is certainly not the case. Something different is going on here.
The MasterFlat is definitely not saturated. Statistics tool says maximum = 0.574. After a split into CFA channels, the results are (in the Statistics process 'Unclipped' is disabled):
CFA0 CFA1 CFA2 CFA3
count (%) 100.00000 100.00000 100.00000 100.00000
count (px) 2923592 2923592 2923592 2923592
mean 1.484427610e-01 5.348702580e-01 5.349518453e-01 5.358891165e-01
median 1.494930387e-01 5.369691252e-01 5.370509623e-01 5.383101701e-01
stdDev 5.705807990e-03 1.809740888e-02 1.808897539e-02 1.673962951e-02
avgDev 5.592659166e-03 1.778350117e-02 1.778313594e-02 1.640620176e-02
MAD 5.509970383e-03 1.807649392e-02 1.808603787e-02 1.640082490e-02
minimum 5.841452257e-02 4.034291209e-01 4.052959682e-01 4.009656609e-01
maximum 1.614647359e-01 5.729865431e-01 5.740009545e-01 5.712071060e-01
The CFA1, CFA2 and CFA3 channels are very close together, but the CFA0 channel (red) is weak. This is due to the light source and the high sensitivity of the sensor for green light.
The strongly different illumination of green and blue versus red may be not optimal, but in my view, the MasterFlat is not the cause of the problem.
(Besides, your flats were calibrated with the setting 'No normalization' in the section 'Pixel Rejection (1)'. Recommended is 'Equalize fluxes'. - However, this will not be the reason for your issue as well.)
Does the integration of light frames (that is: BEFORE applying DBE) also show this artifact?
If yes, repeat the ImageIntegration step with the previously checked input files (fully calibrated light frames).
I also have an ASI294 and in my MasterFlats the red channel is also weak, albeit not as extreme as in your MF. I never saw a problem like this before.
Bernd