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do not know how BOTTOM-UP is

do not know how BOTTOM-UP is interpreted by software you use to check. If rows are reordered, but Bayer pattern is not, this will result in incorrect demosaic.

It is just a flag to switch Bayer Pattern to match the right one, as you said ;). And in the cae I save in TIFF it is not used.

Try to output files with even row count. If my hypothesis is right, this will result into the same behaviour for both cameras.
I thought it was something like that. BUT ....
I can notice inconsistent behavior between 1200D and 1300D where the (effective) image size is the same (5202x3464 pixels) and even.

Maybe I'm doing something wrong, but ... I don't see what and where as I apply the same process to each image.