They aren’t using a headphone when performing the measurements, so it doesn’t have to be redone for each headphone. It’s basically measure speaker FR in ear, measure speaker FR free field, calculate HRTF based on the difference.
If the technique weren’t useful for headphones, I’m sure oratory1990 would say so. 
Yes, but they’re using a headphone when applying the HRTF information to… correct the headphone. 
That works out better if you include information about the characteristics of the device you’re starting with, especially wrt. the size of its membrane and its position relative to the eardrum during use. Griesinger’s method bakes this in without special efforts or extra devices. In fact, bjorken22’s method could get there too: he just needs to measure in-ear when listening to speakers and in-ear when listening to the targeted headphones, and subtract those two from eachother. Then there shouldn’t be any need to add the -10 dB bass tilt manually (he initially gets it in both his measurements but then subtracts it away), or do any other guesswork-based manual corrections.
That isn’t saying much, Oratory is someone who has done staggering amounts of work based on the flawed premise of a single headphone-specific EQ profile (with no listener personalization) being able to provide a “flat” FR, or “neutrality”, or “transparency”. But as Griesinger has shown by comparing equal-loudness tunings made by different people, all with the same headphone, individual ear shape differences change the sound so much it’s nothing short of ridiculous to claim one EQ profile could achieve neutrality for everyone.
They’re using it to determine the FR target when using the IE microphone to measure the headphones. So yes, the measurement of each headphone needs to be done. But the procedure to determine the target does not.
It’s a common misconception, but oratory1990 has never claimed that his EQ presets provide a flat/neutral/transparent experience or that they do not need to be personalized. In addition he is a trained audio engineer who designs headphones for a living.
I didn’t mean to be dismissive of your statement about the IE microphone’s position though. For sure, ideally you’d be measuring at the eardrum. So the target, as calculated, will need to be adjusted. Just as bjorken22 noted, it is a starting point.