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The mixer strips (and sequencer) highlighted has been my great template frustration.
Although a QSS expression like the following should work, it doesn't:

qtractorMixer qtractorMixerStrip[selected= "true"] {}

What you propose about forcing it to be a specific color of the color theme that is not affected by "relationship between the midlight and base colors" may be a practical solution... but limited.
(I think it would be nice if something like this was implemented in official Qtractor. The current automatic behavior "midlight and base" you mention I think is intended to avoid conflicts between dark and light themes. But not only does it not solve it, but it makes it unpredictable and difficult for the user to solve it themselves by selecting the colors they consider most appropriate.)

I still don't know why it can't be accessed by QSS, which is the real solution.

I even tried modifying Qtractor code to see if I could make it highlighted accessible, but I didn't succeed.

In the end I decided to accept that it is a limitation of customization, and make customization possible within that limit (in this case playing with the midlight and base colors of the color theme).