You can only open multiple bookmarks at once by putting them all in a folder, right-clicking the folder on the Bookmarks menu or the Bookmarks toolbar, and selecting Open All in Tabs. Then it only disappears when you click away from it. To make it stay open until you're done, go to about:config, then find, set it to false. If you like to select multiple bookmarks at a time to open, you'll find it annoying that the bookmark menu closes after each selection. Once FF is running, a single click opens one tab in the current window, a double-click opens two tabs (of the same page) in that window. You can't assign the same keyword to multiple bookmarks. I'm running FF 50.1.0 as well, and I'm still having the issue clicking from Thunderbird: Without FF running, a single click opens one window in FF, a double-click opens two windows (not tabs) of the same page. Assign your frequently accessed bookmarks a unique keyword (use just a couple of letters) and whenever you type them into the address bar, the whole site loads. When you click on a particular bookmark, the info at the bottom includes a keyword.
You can use this window to control the tags as well.
To make those folders, click the Bookmarks menu and select Show All Bookmarks. That's a little bit of extra organization for your bookmarks beyond the folders you'll want to make. But take note: when you make the bookmark, the menu that drops down gives you the option to tag the site. My next thought was to use ctrl+click, middle-click, or right-click 'Open in a new tab', but you seem to be aware of all of those. Click the star icon in the address bar when visiting a site, and a bookmark is saved. It looks like I open items in new tabs for almost everything else:, ,,.