Booxtor, if this feature, together with multitasking, will be implemented in the next firmware, then I will look forward to it: for my needs, they would be a HUGE improvement!.
I am sure you will do it for the best, but if I may dare a suggestion, this is the way I would do it (for settings):
in the internal user space (the one which gets usually mounted on pcs), create a top level hidden dir named, say, .files_settings.
Inside this dir, on file for every regular file, with its settings: bookmarks, last page, fonts, zooming, reader and so on.
The name for the settings file of a file should be the name of the file itself plus some extension to avoid homonyms.
For example, if I have a file named "my-file.pdf", its settings file should be
where 463464 are, for example, the last 6 digits of its md5sum: this should be enough to avoid homonyms.