That is true about most double stacks, but you can still put 2 dots on the back (or side) for #2, 3 dots for #3, then start putting them next to the correct number. Number 1 still has nothing.
There is also no rule that says you have to start at number 1 - I gues if you have more than 11 HK Mags you might run out of witness holes
To distinguish all of my mags I have had to resort to over marking. I fill in the S&W logo on the front, I fill in the mag number that corresponds to the magazine number, and I mark the baseplate. I also use pink, it is very visible.
I don't mark the baseplate, I number the magazine body itself, usually with a silver paint pen for dark mags and a blck Sharpie for light colors.
"PLAN FOR YOUR TRAINING TO BE A REFLECTION OF REAL LIFE INSTEAD OF HOPING THAT REAL LIFE WILL BE A REFLECTION OF YOUR TRAINING!"
For AR mags, I use a sharpie designating my initials, mag number and in some cases ammo type (MK 262 Mod 1) or (MK 318 Mod 0).
Pistol mags? Silver sharpie on M&P / Glock mags designating initials and mag number.
Very unsophisticated, but it helps me keep track of my mags.
I number as well; but I also use a zero-index. The first mag is always #0, because that mag becomes the "control" magazine for reliability testing.
What makes it the "Control"? Do you use it less? Always download it?
With any given group of OEM Mags there is no reason to expect any one is more suitable as a control than another; and if they are all used the same way there is, again, no reason to expect any one to be more reliable than the other.
I originally started the system with 1911s. Back when I first did it I had one Wilson Combat mag that I used as my reliability standard by which all other mags were measured, since 1911 magazines can be a real mixed bag. With mags for modern production guns like my M&P, I still use the zero index mostly out of habit and vanity these days.
Also, I still have that Wilson mag, and it's still running.
Those are my mags in the picture...so yes I number them all