With Sibelius, one can easily start and stop a staff mid-system (or measure) by
changing that staff to an "invisible" one. Thus, the passage was engraved with
two staves: a normal one for pitched notes, and a second, single line staff
above for non-pitched notes. Instead of placing pitches on that line, I engraved
pitches one line higher (this line does not show, of course) and used
"invisible" noteheads; thus the "extended" stem. Circular noteheads were placed
manually as symbols (e.g. articulations).
My approach with Lilypond thus far has been similar, but I'm having difficulty
suppressing the single-line staff mid-measure or -system: if I change the number
of staff lines to zero, I get a whole host of warnings. Also, placing graphical
symbols over blank stems to create circular noteheads is problematic, as one
then triggers collision avoidance (which, as you say, one should be able to
turn off).