One of the features I have been missing from the Ms. Onenote was the separate windows. After a long wait, now, it is here.

Onenote windows has been very efficient for years now. Slowly, the mac version is also catching up.

The "link to paragraph" feature specially is very useful--link to a specific point or idea rather than linking to the whole document (note). Even Tinderbox cannot do that.

Also worth mentioning that the latest update to Bear includes opening notes in separate windows on the desktop app.

Any advantage of Bear over Onenote?

I see, the tags in Bear seem to give it a better organization system than the folder system in Onenote. Onenote's tag is not as such robust.

The problem with both of the applications is that they are database systems: the noted stored in these applications cannot be indexed in Devonthink; and Spotlight cannoto search them. For the rest, I see no much of a difference.
Of course, Onenote is universal (Windows, mac, ipad, android); and syncing is free. Notes are available offline for free (contra Evernote).

I am feeling that Onenote is becoming a more stable sytem than any of these transiant small companies poppping up and disappearing in a few years.

I agree that Bear's database system is a bit irritating compared to e.g. Notebooks, where notes are kept as separate files in separate folders.

On the other hand, Bear's own search engine is excellent!

A new version of Notebooks is, incidentally, on the horizon...