This little hack made me give Kobo another try:
If you add "ExportHighlights=true" to the "FeatureSettings" section of the devices config file, a menu item will be added to the books menu in in the library list on the device to export them as a text file on the device.
I had to manually add this section to the config file
/Volumes/KOBOeReader/.kobo/Kobo/Kobo eReader.conf
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