I got an AtlasNova high spec laser and it of course has the marks near the button.
Here's what I assume is the deal. If you call Arnold and ask him, he'll say that he does nothing to the lasers, he just orders them in bulk from the Leadlight manufacturer and tests them all. Some just 'happen' to have extremely high outputs and he culls those out and sells them as hi-spec.
My guess is that he has to say this for legal reasons- because to admit that he (or some subcontractor or 3rd party) has popped the button off and exceeded the FDA class IIIa limits might put him in a tricky spot from a liability perspective (similar to the rules we have here on CPF about posting pictures of >5mW used outdoors, etc)
If Arnold asked the manufacturer to just send him raw pointers that didn't go through their final step of tuning to be under 5mW, they might run into import/customs problems, and the manufacturer then would be liable (especially since they have the Class IIIa, <5mW labels on them and they do not have interlocks, shutters, etc).
I don't personally have too much of a problem with this but I can understand how it may annoy a customer who doesn't realize how this works. Especially if he's thinking "I should just buy some $40 Leadlights and I can do my own pot mod, thank you very much".
For me, I'm pretty satisfied with Atlas Novas' customer service and it's worth the extra money (I hope that continues to be true should I have a problem with my pointer in the future).