Thanks for the excellent suggestion Mono. Usually the articles that I read do not have two columns so I never thought about Paper page mode. Annotations made in Paper page mode will merge normally. And by fiddling with the new page margin settings in the most recent update it is also possible to use paper page mode without having to scroll through the page twice (like it was designed to do on two column pages). Excellent!
I think reflow is still sometimes necessary on the i62 (for reading very wide pages that still won't fit comfortably even in landscape view) but using paper page mode and customized margins is the best way to ensure that the annotations can be merged!
Thanks again! Annotating has just gotten a lot easier!