This is the first time I've heard of this recommendation. If it is true, that is interesting. I have never had a piston-headgasket interference problem before, but I am not running the max overbore pistons though either.
Chamfering the piston reduces compression ratio by adding volume to the combustion chamber right where you need it least. Also, if it were not done absolutely repeatably on each piston, you could take more off of one piston than another, making a rough, uneven-running engine. For those reason if I were in your situation, I would be inclined to do the chamfering very mildly or set up on a machine to make it at least equal to all pistons. I would first test to see if the head gasket could fit without modifying the pistons, if it were perfectly aligned to the cylinders using dowel pins. I know these are available to buy for gasser VW engines, maybe they would fit our diesels as well.
Or, if the fit is plain too tight even with the gasket lined up well, if you had a hydraulic head, you could use a 1.9l diesel head gasket that is designed for a larger piston bore instead of a 1.6l head gasket. With that approach, at least then the volume added to each combustion chamber would be equal between each cylinder.