The confusion was the point, yeah.
There seem to be two definitions of retcon floating around. One is that something is first established, even if in a half-hearted way, and then something newer contradicts and supersedes it. The other is that something about the past is established retroactively when nothing about it was previously known.
Calling Khan an Augment seems to fall squarely in the latter category, so calling it a retcon means having to call other things retcon as well, and having to adopt the second, less common definition.
Then again, establishing cryosleep as an early feature of the Trek universe is
something of a contradiction of a previous fact. What would be so "impossible" about the voyage of the Valiant
if it were standard procedure for crews to survive for decades in cryosleep? Why did the heroes not speculate on the possible survival of the original crew across the two centuries? And why is this treatment of past starflight repeated in TAS "Time Trap" with the Bonaventure
, after our heroes had already been through "Space Seed"?
Since even later episodes dropped even more cues about these things, and they all add up to a fairly consistent whole, calling cryosleep a "retcon" is IMHO excessive. But perhaps not quite as excessive as calling Augments a retcon.