For French, I like having a 4th alphabetical key under the middle finger (for instance, move the innermost thumb key a little upward so that is contiguous with the middle finger column). This allows having all the most common characters in the main layer (also using most of the outer pinky columns for this purpose).
Otherwise does this 2 row cluster work well for you? (In particular the upper row)
Concerning the technical trick with xmodmap, I have the feeling you are adding much complexity just for the sake of using qmk’s graphical configurator. Since you are already using xkb (obviously, since there isn’t any serious alternative under X11 or Wayland!), why not configure everything in xkb layout? This way you can configure any existing character without any strange workaround or third party tool! Then your use qmk just for fancy stuff (layers, combos, hold-tap, … ).
The usual argument against xkb is that you cannot bring your keyboard around and have it ready to use on any machine. But since you are using xmodmap, I assume it is not a concern for you, is it?