Some musings about the scenario as portrayed in TWoK:
As for how the confusion came to be, I'd share the blame evenly.

After all, TWoK shows that there were Klingons at Gamma Hydra, while "Deadly Years" shows there are Romulans there and it's their NZ, so the TWoK writers should hang. The
Star Charts basically suggests the Klingons were in Romulan space - perhaps as allies of the Romulans, perhaps in order to frame the Romulans and cause a Rom-Fed war - but since the bit about Tezwa contradicts this, the suggestion is wrong and I should hang for making it.
Perish the thought, there shall be now
Timo hangings today!
Perhaps the Charts should have been drawn so that Gamma Hydra sits right between the Romulan and Klingon Neutral Zones?
But Gamma Hydrae is real, regardless of misspelling it Gamma Hydra, it's accurate in its placement in the charts. There is, however, merit in the theory, and certainly plenty of precedence in Trek, of names of trek places being bastardizations of scientific astronomical terms and real system names. (Mira Antliae anyone?) Even if they may be repetitious.
Then again, only the "Time to" storyline so far suggests that the KM incident was real to begin with, and if we didn't have to accept that, then the TWoK simulation could be as screwy as the instructors want it to be...
It still is as screwy as the instructors want it to be!
I think that Star Charts is fine, if we can suppose that the Maru simulation is taking place about 40 lys out of Altair then, according to Star Charts, this could easily put it in the Rom NZ. Which, as a hypothesis, has many positive attributes. In neither the book nor the film is the NZ actually stated to be the Klingon Neutral Zone, given that, the fact is that the only canonical reference to any NZ is the Romulan NZ, so that fits the scenario well enough. Combine that with the previously established facts regarding "The Deadly Years" i.e. Gamma Hydra and the Romulans, and the convenient image from TWOK of "the NZ" being a large egg-shaped region, and that dovetails nicely into the depiction in Star Charts.
In the end, I still think I like the newest take on it all the best, even if I might have to speculate that Tezwa lies somewhat closer to Gamma Hydra than I thought...
Timo Saloniemi
The Kobayashi Maru test.
Given its setting on the 23rd Century Enterprise, the appearance of 23rd century Klingon ships, the unlikelihood of the existence of any NZs at all during the pre-federation period at any rate, and unaided by the scene's use of very curious distance and regional nomenclature, I think it's safe to say that the only facts presented in the simulation that we can give any kind of credence to are that:
a. there's a ship in distress named the Kobayashi Maru, and
b. it's a no-win situation.
Almost nothing else in that scene resembles the probable reality of the situation, so common sense should tell us that we really shouldn't rely on any of it to be historically accurate.
There's no contradiction with the bit about Tezwa, that reference is completely consistent with what's shown in Star Charts. The Wrath of Khan simulation is also consistent with Star Charts if one infers the Romulan border, given what was already established in TOS.
However the simulation itself has
never been shown to be consistent with its own historical basis at any time we've seen it. It has always been just a very important, student-agonizing LARP/videogame.
With any of these references, things only become problematic if one assumes any of the events take place at or near Gamma Hydra, which was my messed up assumption in the first place. Looking closer at the film scene, I see now that it doesn't make any sense, and the slightly tweaked version in the novelization even makes an effort to clear that up. So really, no reconciliations need be made.
yet...