Possibly WotC aren't certain which direction to take with B3 either.
The whole background on B3 is uncertain, there's been many versions told over years that are conflicting, some by the people who were directly involved. Whatever the case, there are also known to be actual flaws in the original. But even given those flaws, one could say that Moldvay's rewrite undermines Wells' original work on the project. Some might even say that it's a smoking gun pointing to sexism within TSR at the time, but I'd hesitate to go that far. After all, TSR had a release schedule and something about the module was unsuitable. Some of the things considered unsuitable aren't too unreasonable either.