"I'm cutting an indie feature ... There doesn't seem to be a clear logic to it ... Is this normal?"
for an indie film with a possibly inexperienced sound recordist... yes!
however, are the stereo tracks actual stereo pairs, like a stereo ambience?
that can be done.
and yes, Blank tracks i've seen, but mainly due to a strict adherence to some prevailing logic,
such as character B was not in that particular shot. no sound was needed, but an empty track was recorded to match the other shots for the same scene.
"I was under the impression ... cut a single track of mono sound for the dialogue to start with in the rough cut."
not necessarily.
a lot depends on who is doing the audio post.
while some editors have the luxury of being able to edit with a single mix-down track, that then puts a certain burden on the sound editors who would need the tools (and time) to conform back to the multi-tracks.
the common scenario is that you edit with all the tracks.
and 4 tracks is a pretty small number of tracks to work with!
there's no standard way, really. certainly no way that would be standard across an entire movie.
i know people who will standardise within a scene, as mentioned above.
i also know editors who like to only have an even number of tracks so are happy to get a blank track if it helps.
it might be worth showing some of these tracks to whoever is going to be doing the sound post, and get their input.
nick