You've been around for a very long time, but it doesn't appear that you are very involved in the communities here, so before we get to your question, I'll first go over some basics, to make sure we're on the same page.
First, any user with more than 3000 reputation can vote to close a question. Five such votes are required from normal users, while an actual moderator can close or even delete a question without anyone else's concurrence.
Second, SF has been around for several years and its topic focus has evolved over time, typically narrowing. Most of the questions you saw, such as those tagged domain-registration, date back to those olden times when SF accepted almost any question even if it wouldn't be on topic now. We try to close those as we find them, though there are many still out there, and only 24 close votes per person per day.
Third, whenever a normal user votes to close a question, it goes into a review queue where other users can agree or disagree with the close vote. If enough users disagree, the existing close votes will expire away and those users will be unable to vote to close the same question again. And if enough users agree, then the question is closed (or migrated).
On that note, closed questions can also get reopen votes, which go into a reopen review queue. Questions also go into this queue automatically if they're edited after being closed. So closing a question is not necessarily forever.
With that out of the way, now there's your specific question, and the general issues.
Your specific question regards an issue not often dealt with by system and network administrators. We buy the domain names our companies need, and that's usually that. If someone's squatting on them, we tell the lawyers and they handle it from there. This issue is much more commonly seen by a certain class of webmaster, and so Webmasters is a much better fit for the question.
The question then becomes, what to do with the question? We could answer it, migrate it, or close it. Answering it would just create a duplicate question and answer across multiple sites. While this is often useful, sometimes it's better not to have such duplication. Migrating it, in this case, would leave the migrated question closed as a duplicate on the destination site. Closing it outright, with a pointer to the question on the sister site, was what happened here. Since Webmasters is not on our list of migration targets, actually migrating it would have required a moderator to intervene.
If there had not been an existing question on Webmasters, I would have gone to the trouble of asking a moderator to migrate the question. But since there was an answer, migrating it would have just created extra work for the moderators and community of both sites, for no clear benefit to anyone.
The question could possibly have been answered here, as many of us do know the answer already, but as it might be judged to not be of significant interest to our community, it could then be closed as "too localized" (not necessarily by me, but by others). This also would not benefit you or anyone else.
So I think your question got the best of all the "bad" alternatives.
Now on to the general issues:
I believe your request for "community upvote and downvote of the a moderator's question flags" is already covered by the review queue, so I won't address it further.
Finally, it's my understanding that the Stack Exchange team hasn't been particularly interested in implementing any sort of cross-site search from within individual sites. This has been asked for many times, and rarely or never gets an official response. The only concession to cross-site search has been to implement it on stackexchange.com. (And from what I understand, it's terrible compared to, say, Google.) If you want to pursue this sort of feature, I suggest visiting mSO and perusing the existing questions.
