When Flymake has not yet checked the backend of a visited file it
displays a question mark on the mode line next to its lighter text.
This "?" indicator is fontified with the 'mode-line' face, which means
that it inherits properties such as ':box', ':background', and
potentially others.

The attached patch changes fontification to 'mode-line-emphasis', which
is a face that is specifically designed for drawing attention to such
indicators.

This allows users/themes to maintain a consistent presentation for their
mode lines, regardless of whether they are active or not.

The attached screenshots show the before and after states with all
themes disabled.  Focus on the inactive mode line at the middle of the
screen.

If maintainers think that this change does not provide sufficient
emphasis, I would suggest we look into updating the specifications of
'mode-line-emphasis' instead of using an inappropriate face for
individual indicators.

What do you think?

Best regards,
Protesilaos

-- 
Protesilaos Stavrou
protesilaos.com