It is weird to me that the owners manual just makes the assumption that we know what cart height is. There's no explanation.
Seriously though, all that chart is doing is giving you a starting point to getting the arm level. Place a record on the platter. Now place the arm somewhere on the record, preferably the middle. Now view the table from the side and simply adjust VTA until the arm looks level from end to end.
That's just a starting point though. The real trick is getting the right stylus rake angle. And, unfortunately, a level tonearm does not always lead to the correct rake angle. But, it should get you close. So, start there, then fine-tune by ear. Besides, some people like to run their carts tail-up or down depending on what sounds best to them.
Not to mention, VTA will change with every record you put on, so there's no point in obsessing too terribly much over it, imo. Also, that chart assumes you are using the rubber mat that came with the M3D originally. This particular mat is about 1/2 the thickness of the thick Technics mat that comes with the MK2.
EDIT: For what it's worth, my VTA is currently set at 2mm, but I'm also using the thick Technics mat, which I think is like 5mm. If I was using the thinner mat that came stock with the MK5 (and your M3D), I would need to lower the VTA, probably down to 0 or 1. I'm using the AT440MLa, which I believe is a 17mm cart. Or maybe 17.5, but either way 2 should be just about right. For a while I was running it with a VTA of 2.25, and I may go back to that at some point.