While I have the same problem with the boxes and some I don't see them again as they are hidden in the depth of the closet... I keep them for the same reason as you... BUT...
I don't think that any manufacturer will cut his price if you take it wrapped up in a newspaper...
The box is like a beautiful dress on an excellent woman...
And, some of them are a work of Art, with a loupe included etc
And also a trend is developing among the expensive watches: the box is a watch winder to keep your automatic timepiece always ready.. let us hope that this trend will expand and then the boxes will have a raison d'etre...
Tassos