It used to be possible and I used this very often on Internet Explorer, back in the day when it would save the bookmarks as separate files in the Favorites folder.

Concrete example : let's say I want to move all the files containing the word computer from "Other bookmarks" to a folder called PC. It is easy to do then the PC folder is empty, difficult to do otherwise or if I have other bookmarks that contain the word "computer*, because Opera will search in all the bookmars / bookmark folders for the search pattern.

In order to address this and similar issues, you could implement full path on every bookmark, filtering in local folder, move operation shortcuts... and you will basically (partially) reinvent Total Commander, and that would be pointless.

What I suggest is this :
v1. Open up the bookmarks file format. Publish the file structure. Complicated ? Security concerns and high complexity ? Continue reading.
v2. Create a bookmark import / export add-on that is able to import / export bookmarks to separate *.url files. This is the fastest way to get the full power of Total Commander working for Opera. Minimal complexity but security concerns remain.
v3. Have Opera open access to bookmarks as a FTP server or USB drive that can be turned on / off at will and with user's permission. Harder to implement but once the server is turned off, no traces remain on the host computer, thus protecting user's privacy (like a private window for bookmarks).