Father Bill is correct that each maker has different preferences. If you do most of your kilt buying online, that's where this question hits the grey zone. Based on personal experience; I try to have measurements based on how I will wear the garment most frequently. For example: I wear my kilts mostly with broad cloth dress shirts or similar items. So when I get measured for a new one, I try to get measured while wearing that type of shirt and my p@nts pulled below my kilt waist to ensure an accurate measurement. This is how my mother (a professional seamstress) recommends people get measured. The more layers one has, the more guess work there is to the measuring. I was measured once in a kilt, and my waist was about two inches off the true measurement. Two inches isn't much in a great kilt, but for the tailored modern kilts, it's the difference between kilted perfection and sagging aprons (or worse).

Just my two cents.