Hi Andrea,
Since I've never explored this context in detail I do not have the explanation you're looking for.
Anyway, here are two workarounds; none of them are good but, at least, do the job :
\version "2.18.2"
\new MensuralStaff {
\relative c' {
a b c d e f g a g a a g a a \bar "" \break
%r2
\tweak Stem.stencil #f
\tweak stencil #(lambda (grob)
(grob-interpret-markup grob
(markup #:musicglyph "rests.1mensural"))) a2
a4 f
}
}
\new MensuralStaff {
\relative c' {
a b c d e f g a g a a g a a \bar "" \break
\once\hideNotes\grace a4
\tweak extra-offset #'(-6 . 0) r2*1/2
a4 f
}
}