I've been googling a lot but could not find any instruction for passing the "Volume Purchase Program" option when submitting an iOS app to iTunesConnect using fastlane-deliver.
Does anyone know if it's even possible?
You can not do it from fast-lane itself.
Here is the options file of fastlane project.
https://github.com/fastlane/fastlane/blob/master/deliver/lib/deliver/options.rb
As you can "not" see, there is no field to change B2B option there. Unfortunately, it seems you should manually change this.