I’ve been endeavoring to use MarginNote annotated files in Tinderbox for some time. It’s not an easy undertaking for various reasons, but I hope it’ll get easier in the future.
I’ve found that the greatest hurdle lies in the problems with MarginNote’s exports. While many users here appreciate the many formats that MarginNote provides for exports, there are many glitches with the final export files – especially for DEVONthink, RTF, and OmniOutliner files. I think that @jprint has summed up many of those problems in this and other posts. Suffice it to say, I fully agree with his points since they greatly affect both the integrity of the exported files (and therein annotations), as well as the ability to use said files for inter-app functions, such as MarginNote-exported annotations in Tinderbox.