> Stefan, is there a way of avoiding this effect, perhaps by using a
> function in whitespace-font-lock-keywords?

We could of course replace the regexp with a function and thus do
"whatever we want", as in:

       ,@(when (memq 'missing-newline-at-eof whitespace-active-style)
           ;; Show missing newline.
           `(,(lambda (limit)
                (when (and (re-search-forward ".\\'" nil t)
                           ;; Don't mark the end of the buffer if point is
                           ;; there -- it probably means that the user is
                           ;; typing something at the end of the buffer.
                           (/= whitespace-point (point-max)))
                  (put-text-property (match-beginning 0)
                                     (match-end 0)
                                     'face 'whitespace-missing-newline-at-eof)
                  nil))))

But personally I think the root cause is the use of OVERRIDE and I'd
replace it with `prepend` as in the patch below, but whitespace uses
OVERRIDE "everywhere", whereas my argument would suggest it should use
`prepend` at all those places, which is likely beyond the scope of `emacs-30`.


        Stefan