Responding to one of my own questions (#5) above, it appears as if general and more open ePub annotations are still a work in progress (even in 2014). Two competing standards seem to exist (
http://www.openannotation.org/ and
http://www.idpf.org/epub/oa/).
I've discovered that I can setup Moon+ Reader Pro to sync my annotations and reading position, but they're saved in its proprietary format.
So until there is some consensus on annotations and support in e-readers, I'm still interested in knowing if there is some e-reader software that will write annotations in a text-based sidecar-type file at the time of me making an annotation, so that I don't have to remember to export annotations later.