My understanding (somewhat superficial, I'm sure) is that the transmission (i.e. the sources) for most of Buxtehude's organ works is rather problematic - multiple, conflicting sources, by many different hands, and few by the Buxtehude himself. This means that sometimes editors just don't have the evidence to decide what was the composer's intention!
My approach would be to (a) try and decide what I thought worked best musically, and (b) see whether the recordings I could access agreed.
But whatever you do, have fun - Buxtehude is great!