[RPG] How are the skeletons in Tresendar Manor created? And by whom

This seems to be a case of the creature description being based on a development version of a spell that was changed before publication, but the bloody skeleton's ability wasn't updated to match. Or the design notes for the bloody skeleton read something like "or 0 hp on blessed ground" and the developer that actually wrote the text didn't do due diligence in translating that into the correct spells. However it happened, it's an error rather than a mysterious rules interaction.

Go with your gut, and change it to "the area of a consecrate or hallow spell". Pathfinder and d20 system games in general expect GMs to make their worlds believable rather than to slavishly follow rules into weird contradictions and twisted corner cases that break suspension of disbelief, so you're entirely in the right to change this in your own games. If you're a player in another GM's game, suggest the fix as a sensible thing to do, but leave it up to your GM.

Spoilers ahead:

The most information we can get from the book can be found in the General Features section of the hideout description, in the box titled "What the Redbrands know" (page 20):

The Redbrands have a handful of captives in a holding area "near the old crypts," which are guarded by skeletons (see areas 4 and 5).

This only tells us that the Redbrands are aware of the skeletons (it's their trap after all). However, it is likely that at least some of the Redbrands would know the command word as well, as the trap is positioned right in front of their prison, and the skeletons might otherwise interfere with prisoner transfer.

If this doesn't seem likely to you, there is at least one person in the hideout that is expected to know such things: Glasstaff himself. Though it is not strictly specified in the book, it is very likely that he's the one who set up the whole trap, and thus would know the codeword.

As for how could your PC-s find this out? Interrogation, persuasion, magical effects, and others. While getting information that you don't ask for in an interrogation seems unlikely, a particularly successful one could yield it. For instance, if your PC rolled an Intimidation check while interrogating and got a very high score, an NPC might be so scared that he starts spewing out everything he knows (possibly pissing his pants at the same time). Or a well worded Suggestion ("Lead us safely through the hideout") spell might prompt an NPC to divulge such secrets. It's even possible to make allies out of enemies, and an ally would be incentivized to keep his new friends safe from skeletons.

As a side note: the adventure book you're using is not a rulebook. It is merely a suggestion on how to play the adventure the way the author imagined it. DM's are allowed (and required, imho) to adapt the adventure according to how the campaign is going.

Sticking to the book is handy for new DM's that are still struggling with all their other responsibilities and don't want to add adaptive storytelling to the list. But the book was not meant to be a cook book, so there are naturally some holes in the text that the DM is required to fill in. This is also good practice, as modifying the initial script in reaction to PC's actions usually leads to a much more enjoyable campaign than just going by the book.

In short:

The PC's might not enter the skeleton room at all, at which point the keyword is irrelevant. It is also irrelevant in case the players stumble upon the room before gathering any information. But it's good for a DM to know it exists so he can throw it in at any point in the game where it would make the game more enjoyable (as a reward for a high roll, or even as a new plot point that enriches the original adventure).