This will soon change in VemsTune and the cylinder numbering in the ignition order can be defined to make it easier to set up the related tables (ignition, injection, ref tooth). It will also help the individual power gauge, to easier find cylinder with problems.
It might be a few weeks or a month at least, not certain yet but it's on the developers priority list right now. It needs a small change in firmware, only a list of cylinders - the largest change is in VemsTune and how it presents this to the user.