Thank you, Froyok, for your suggestion.
I did new attemps to take it into account.
In detail, and if we refer to the example in my first post :
I ctrl+drag succesively the two materials on the red cube (the left one), and the layers tab takes on this aspect :

If we focus on the alpha mask, we can observe that the white and blake zones clearly respect the red/blue zones of the ID Map. That's why the blue cube remains white. And that's good.
Now, I drag (
whithout pressing the ctrl key) the smart mask over the 'rust fine' material on the layer tab.
And here is the result :

Again, if we focus on the alpha mask, we can observe that the smart mask is applied over the two parts of my object, so denying the ID Map.

To workaround with this problem, I apply this solution :
- right click on the alpha mask
- on the contextual menu choose 'add color selection'
- on the 'color selection tab', click on 'Pick color' and then on the blue cube (the one on the right)
- on the 'color selection tab', set the 'Output value' to zero -completly blake-
Et voilà :

Focus on the alpha mask so modified :

Such a workaround is however not so easy to apply if we imagine that, in addition to the blue cube, there would be a yellow cube, a green cube,...and so on.
Vincent