Think about it like this--when you use a CD to seal the earcup, the surface of the CD is supposed to be the side of your face. Then you put the testing mic at the hole of the CD, and you shouldn't push it in, because that wouldn't make sense--it's like your eardrums are coming out of your ears.
But of course, this isn't totally scientific/precise, because the ears actually have ear canals to shape the sound, while a CD/testing mic cannot emulate the existence of ear canals. Also, the side of the face around the ears are skin and hair, while the CD's surface is much more reflective. You can maybe line the surface of the CD with something like cotton or whatever that's closer to skin/hair.
I have used the above measuring method to measure my headphones, but I have not used ARC to measure/tweak the headphones, because I'm not sure if the result will be accurate, as ARC was never designed for headphones. I might give it a shot one of these days though, just for fun. But since I already tweaked the custom EQ curves for my headphones to perfection, I'm not in a hurry to try it out.
You might want to take a look at this though:
SonoReplicator - MP3 demo
That's almost like IK Multimedia's ARC System, but can be used on headphones too.
I almost laughed when I saw them using the measuring mic through the hole of a CD--since that's exactly how I measure my headphones too.
You should get caught up on the new developments in Planar Magnetic headphones. It's now been revolutionized and making a huge leap in quality/capability through products like the Audez'e LCD-3, LCD-2, and Hifiman HE-500, HE-6, HE-5...etc.
Also, the progress is typically evolutionary, even if the technology is fundamentally the same, many advances through computer simulation, better testing/measuring techniques, superior material...etc have made advanced that weren't possible in the past (or weren't cost effective).
For those of you who are thinking of the M50 or already own one, I can share my custom EQ curve for it, which turns it into a more neutral/accurate headphone.
You do not read headphone frequency response graphs the same way you read ones for speakers. You should read the educational material provided at HeadRoom--it explains how to properly read headphone frequency response graphs.