Matt,
I don't see it as a major concern although it would be good to have a common methodology. Either on the form or corresponding procedure you could put some type of disclaimer:
ie
"All non-applicable fields must be filled in with N/A"
"Blank fields on this form are considered not applicable"
I think as long as there is a common understanding there would be no internal or external (registrar) concerns, if you can justify and document your position.
ASD...