Unfortunately, it seems to now be taking a very, very long time to do this when I have a lot of tabs open. It used to take minutes or less, and now it can take up to several hours. I'm not sure what's causing it.

To your first question, no there is not a (built-in) option to rename the folder after creating it (like a popup or something). That would defeat the purpose of this extension. You can right click the folder after bookmarking if you need to rename it something other than the default value you already chose on the options page.

In the latest version (2.3) there are also options to automatically save (into any nested folder you chose using the default name value) using the current day, date, time, include the active page as part of the folder name etc). Unfortunately Opera is very bad about passing updates through. It can sometimes take months after submitting to them, or never at all and they don't provide any explanations about this.

You can use Chrome extensions via Opera (just search for "Install Chrome Extensions" in the Opera store if you don't already have it). I would recommend installing that extension then just using the Chrome version of Bookmark All Tabs and all other extensions. Also, do visit the link above where the most up to date documentation can be found on all the cool stuff that can be found in the latest version.