They are at a price....
It's been suggested that very early ones sold (well before Adorama) were 6 screws.
The innards between the 6 screw and the SE v1 are different. Reprinted my list (cleaned up - post #372 - at the end of this post). Some of the changes don't individually change things *much* but in total, they do.
The largest difference most agree is that the 6 screw has along with the Phi 1266 the fastest rise time/impact of any headphone in the bass. It's clearly 11/10 in that regard. The SE doesn't have it. It's very nice, better than most - esp at the Adorama pricing, but not the same. If I could point to one physical change between the two models - it's the 6SE has a lot more glue on the inside facing stators - which might hold the whole assembly tigher and not allow the same level of excursion in the bass. Like to see someone cut some of that away to see - but I'm not offering.
The other sonic differences which are more subtle and not a matter of common agreement is that to me: the highs of the 6 screw are etched/grainy) not ethereal - more rnging? The mids are smaller in soundstage and volume (giving it a percieved deeper stage), and its a bit dry. It has good dynamics. Detail is good, but bettered by other cans these days. It's possibile the glue issue by cutting the excursion is tamping down on ringing.
Differences between the HE-6 6 screw and HE-6 SE "v1":
Cable: 6 screw - 4 core OFC different vs. the "classic" surgical tubing of the SE v1. Have not A/B'd the 6 screw cable, the one I used had a patina on it. I did blind A/B the 6 SE "v1" cable vs Custom Cans low resistaance cable - both XLR's and the HFM was audibly different and not in a positive way.
headband different: clamping force harder on HE6SE, pads could also lie differently on the head per dimensions of headband. Hard to prove/test but could be audible. 6 screw headband prone to breaking, and heavier as well.
Pads: 6 SE came with the pleather and felt. The SE came with the "pali pad" designed for the Sundara. All 3 towards the bottom of the dozen I've tried - but clearly different from each other re: tuning.
Body: different material, different resonances. At least subtle audible differences.
Damping: The HE-6 came with 1/4 round damping, SE not; medium->big audible differences
Safety bar not present on HE6SE; cancellation/resonant issues, I've got sliver of felt on my HE-500 safety bar and its audible, but not a big change.
inner facing magnets cut differently, more glue used on HE6SE; do they block the direct output of the membrane, or cut its excursion. Possibly a big factor.
Magnets same strength?
Membrane same thickness? I believe it's thinner on the 6 SE - also a likely factor in the sound.
HE6SE a bit lighter and more comfortable.
They are not physical or sonic dupes of each other, not that close despite what some earlier reviewers opined (early 6 screw 6 SE?).