This is not a bug, just how Bookmarks work. They are always relative to the actual virtual playback range, not anything else. From a playback standpoint its the most intuitive too, if the bookmark says 04:00, then resuming the file will also say 04:00, and not suddenly 03:00 or w/e.
Changing this would require a lot of changes in MC, not to mention that it would break everyones bookmark of content with a playback range.
Its also somewhat important for streaming/transcoding, where a player getting a transcoded stream may not necessarily know about the playback range, it just gets a stream from start to finish (where MC applied the playback range already), and needs to possibly apply a bookmark to that - today that is trivial, without having to parse and understand the playback range, which would be a breaking change for all third party clients.
So, just accept it how it is.