Don't get worked up about it. IMHO this situation is very common when it comes to rules questions. A player does not like a DM's ruling and they come to a forum hoping to prove the Final Arbitor of the game is somehow wrong.
This time the op has some decent ground to stand on TBH. Really it hinges on how literally one reads the Evil Domain Power's Text.
Actually, I did want to see if I could prove a theory I have, which I think I did. Specifically if you post as a player, you garner a different response than if you post as a DM. Case in point
this thread. Both are similar in that there is ambiguity in the way the rules are written. Is the same named spell really on a clerics spells list that is on a wizards spell list? Especially when you consider all the level differences, etc. that exist in the game? But the way it's written is the way it's written. Similarly, is an increase of caster level really everything related to said spell? Or does it only apply to things "that don't make your character more powerful". Set happened to provide graphic evidence to support it, but hey those things happen. As you say, don't get worked up about it.
FWIW for the wand question, I ruled that both divine and arcane casters can use a wand that has a spell on their spell list, regardless of source.
For the animate dead question, DM hasn't ruled on it yet, though I suspect he's going to rule for and against it (read on, I explain the waffling) based on the following premise. The caster level increase is applicable at the time of casting and for the duration of the spell. Since animate dead is instantaneous, OK at the instant the spell is cast your caster level is increased. But then it's back to normal, and now you have a problem (not really, I mean they just stop being under your control, rebuke them or turn them lose on the innocent villagers, no big deal) if you are over your limit. That's just my best guess though, technically it does increase you limit, but practically it's irrelevant because the spell is an instantaneous duration. It's too bad that there is no definition of how many HD you can control that isn't tied to a spell description, as that would definitely put a stake in this discussion (little undead humor there to lighten things up).
Finally, ENWorld has never been a final arbiter of the game. Nor has WOTC or the sage (which cracks me up, we've emailed the same questions and gotten different answers each time). The dude behind the screen is the final arbiter. That's why he sits there and the players sit elsewhere. Enworld, WOTC, the sage, etc. are merely additional sources of information through which the DM can use for research and consideration in making their decision.
Thanks!