I agree with this though I wouldn't go so far as to call it a particular "version". I'd say regardless of the similarities the closest it could be called is a "counterpart", and in some respects that might be a bit of a stretch. That said I very much understand where you are coming from.
The reason most bring it up is largely because of the coincidentally similar settings involving a German (or in the other's case, an overall Axis) victory in World War II as you have mentioned, along similarities involving a Europe that's not doing too hot and a balkanized Russia. They're two completely different settings involving a some form or another of victory for the Third Reich, one being more focused on a story-based narrative and a largely bleak Cold War setting, and one that's more down-to-earth (e.g. along so much else, there is no Operation Sealion, a memetically contentious topic on this site to say the least) and while also grim can be more optimistic than the first in a number of areas.
I don't know who started calling TWR a "version" or TNO, in contrast it's like essentially calling the latter a version of the former, something that the fanbases of both would reject out of hand and something that is just as true as calling Thousand-Week Reich a derivative work of The New Order, as stated above. For everyone else, they're two different settings with two considerably different fanbases (with said bases having a small overlap here and there), and one overshadowing the other for various reasons. And one fanbase, of course, that's notably less "edgy" than the other, but that's very much another discussion for another place and time.
In short, I agree with you! Comparing both works is largely pointless, given that aside from certain elements in the setting, they are, at the end of the day, different works with entirely different teams, personalities, end goals, and minds behind them. I know there are those who like one and those who like the other and so on and so forth, but recognizing they are entirely different universes with entirely different points of divergence and ripple effects and takes on the concept of a German WWII victory for different reasons altogether is something I feel a number of people who seek to compare the two works ought to take in account before doing so.
I'll gladly take it if it means I can reunify Yugoslavia with Tito, which it looks like I can.
