Actually, it is an Opera issue after all. I contacted Xmarks support and they said they can't fix this since Opera hasn't released any bookmarks API that would allow them to support Opera. That's why Xmark doesn't list Opera as a supported browser.
I'm still in the dev channel (v27) but I haven't had any bookmarks disappear on me. I imported them over from Opera 12 and have added a number of them since then and everything is working as expected. I've found 27 to be surprisingly stable for a testing release.
In the same way? You mean you want to open many tabs when you start the browser? If so, just add more entries to the list I mentioned. If not, then I don't understand what you are asking and will need more clarification.
If you can make that txt file into html, then import the html bookmarks file into Chrome. (Go to Settings in Chrome, Users/ Import Bookmarks and Settings/ and choose from Bookmarks html file). When you have imported the html file into Chrome, then just copy the bookmarks file from the Chrome profile over into the Opera profile.
Note that the Chrome extension downloader was made by Opera. As for why specific permissions are needed, keep in mind that even a minor thing that is affected by permissions will trigger that permission requirement. The Lifehacker article was quite informative.