I've always felt (and I'm not sure if anyone involved has even given their thoughts on the relationship between the two films beyond a general dislike for the first one and the need to do better) that there wasn't an intentional effort to wipe out/ret con TMP when they made Khan as such. At least not in the sense of that episode of Voyager which is supposed to contain dialouge that is specifically there to say "Threshold never happened".
I think everyone was pretty unhappy with the first film (though the paying punter can more than disagree) and just decided to ignore and do their own thing for the sequel. Which might sound the same as deliberately overriding it but there's a subtle difference in that Bennett and Meyer just did what they thought was best, if it fitted in with the first film fine, if it contradicted it, fine. But either way they weren't that bothered and likely didn't notice because Paramount were unlikely to be encouraging them to use TMP as a reference point (again, fairly or not).
To a certain extent, there was no need to out and out officially retcon the first film whatever the studio thought of it because we're just before the breakout of home video. Any slight discontinuity between the two films wouldn't be a problem for most of the audience because it would have been nearly three years since any but the dedicated fans would have seen the first film and the memory gets hazy.
That's a get out clause not really available anymore (and Trek wasn't the only film series to use it, the Planet of the Apes movies for example tweak the details of their future history with the absurdity most of the viewers won't remember the exact details as well), so you get things like the last Rocky film being released with Official Statements some of the previous sequels didn't count because there was more than a good chance the people going to see it had the DVD set on their shelves and would have even the bad movies much fresher in their minds.
Whatever the actual thinking, I do think it's actually a pleasent surprise (at least for us anal fans) the two films fit together as well as they do. You may have to squint a bit and use some lube but things could have been a lot worse considering the attitude towards TMP at Paramount at the time.