>> Could you try to remove all isearch-related code from wdired.el
>> and see how it reuses dired setup?  I tried, but query-replace
>> proposes to replace matches outside of filenames.  This is because
>> query-replace uses isearch functions, but dired-isearch-filenames-setup
>> is not called.
>
> Are you sure?  Is it not because dired doesn't set
> `replace-search-function'?

Ok, could you try this patch.  Please note that the value 'dwim' of
'dired-isearch-filenames' is used only at the position where WDired
is activated, not at the position where query-replace is started.