1. I think they are the same. I never indicated what type of clearance when I took mine.
2. I think this is only required if you have documents with you name misspelled on it. Otherwise just leave it.
3. As far as my experience goes, you don't need to pay online. You only need the reference number. When you arrive at an NBI branch they separate people who are already paid and who are not yet paid. Paying online will only make you skip one step (which is paying physically).
Sidenote: There were also people able to walk-in when I went to the NBI branch near me.