Difference blend mode and Fill

I have found some odd behaviour with Difference blend mode and Fill.

After a some testing I can reproduce the effect with a very simple edit.

I open two raw images as layers in Photoshop.

I then set the top layer to "Difference" blend mode and reduce the Fill to 50% to produce my final master image. The bottom layer is unchanged.

But here is the problem - the image is changed if I try to Merge or Flatten the image or save it as a JPG.

I have tried various ways of flattening the image - Merge Down, Merge Visible and Flatten, but each alters the appearance of the image. Ctrl+Alt+Shift+E also alters the image.

Launching Photoshop from Lightroom does not help. In Lightroom: Edit In > Open as Layers in Photoshop..., make the edits and then save back to Lightroom, the image is still altered.

In each case the altered image has reduced contrast, reduced saturation and some hues are shifted. These altered images are visually identical.

I have checked my Photoshop settings:

Colour space settings in Photoshop are: ProPhoto RGB, 16 bit.

I have "Preserve Embedded Profiles" for Color Management Policies.

Missing/mismatched Profile options are all ticked.

The original files are raw (CR2) and Photoshop files are saved as TIF.

The monitor is colour calibrated.

I get the same behaviour in both Photoshop 20.0.1 and 19.1.7 on my Desktop PC and my laptop. Both are running Windows 10.

My Lightroom is Classic CC 8.

I do not get this behaviour if I open JPGs as the layers.

Can anyone suggest why I am getting this strange behaviour, or suggest a solution?