Generally, there is no and there never was an issue with metaphysics questios. Anixx just tried to mix things up, discredit fundamental physics, and get attention as it started. The negative votes on this and this question, as well as the positive votes on his answers to the polling question, say that the communitiy disagrees with Anixx that there even is any general issue with philosphical questions on physics SE. Generally, most of the topics he meantioned are not (only) metaphysics or philosophy. Such issues are now investigated by serious theoretical physicists today. So questions asking about such things can well be incorporated into physics SE, if they are appropriately stated by alluding to the corresponding physics theories that deal with the issue, etc
So in my opinion, the only thing to do now is to close/delete (was there not the option of migrating too?) specific questions about the topics Anixx mentioned if and only if they have attracted enough close/delete votes or sparked a huge number of complaining flags and otherwise leave them alone. I thought the system deletes/closes questions automatically if enough votes from mods and high rep users have accumulated (?), so probably nothing has to be done.
There is certainly no reason to generally delete/close larger groups of questions or disallow certain topics in the future as Annix tried to achieve. Neither is a metaphysics tag, saying that certain questions are not physics, needed here. Off base questions should be dealt with case by case as they come in (and as it was done before).
Once and for all, things were just fine before Anixx started to create an artificial issue, so it would be best to leave things allone.
Another point to consider is that refering to fundamental physics questions, that are investigated by serious theoretical physicists today, as "metaphysics" or even worse condemning them as off topic here on physics SE would lend support to people who attack fundamental physics not only in the internet but actively try to prohibit research into it even in the "real world" ...