I read that whole thing with Puerto Rico. That is
not an "unofficial variant." It's not a "variant" at all. The rules state those things are done simultaneously, which is how it was implemented. The rules also state that if the players feel they need to, they can basically request that it be done in order, and that is not enforced by the implementation.
But there's no variant there!. I'm sorry, but I think it's silly to call it that, and I think you're trying too hard to drag up an example to prove your point.
The argument on Puerto Rico is not about implementing any variant. It was more about whether the turn order situation should be forced by the implementation. (Which to me sounds like a disaster when playing turn-based -- it's just going to add a gazillion more "in order" turns that run the game longer. I could see the point of making it an option, but I can also see the point of why it could cause some problems. i.e. I can see both sides. Did it occur to you that Een simply disagrees with you on that point?)
You can argue that the site does what it wants. Of course it does. But that's a lousy example to use when you're trying to argue about them doing unofficial variants, since it's not one. I have no way to interpret the issue with Takenoko, because not knowing the game, I don't have any idea what that discussion even means, but I do know it was stated they discussed it with the publisher.
Yes, I'm totally aware that they don't always say what they mean and are not always forthcoming about things, and sometimes they give some really strange excuses for things. I won't argue with that. (Though it's just as bad dragging Puerto Rico into it under the guise of a variant.) But in the end, they have an agreement with the publishers and I can see it being totally legit to not do unofficial variants.
Sounds like your real issue that they don't want to do more work. Would you want to? Messing with games that have already been implemented can be a real bear and can also be very time-consuming. So not wanting to add to the work load is totally legit. Trying to dig back into an old game can be rather time-consuming, not to mention always opening the door to new bugs, etc. Are you volunteering? I'd rather they take better care of the site overall than worry about variants. (Not that I think the site always runs great - just saying that would be my personal preference.)