First, Evernote uses their proprietary format to manage notes, so, in order for Reader to display Evernote's notes, they have to be converted to either ePub or PDF, the file formats Reader support. Or Reader needs to include a dedicated Evernote app supporting entire service and application features. But I think we have the former case.

For those annotations and images being uploaded to Evernote from Reader, as mentioned above, will be convered to Evernote's proprietary format. So, technically they could be downloaded back to Reader only by being converted to ePub files.

I think the purpose of support for Evernote is to provide mainly a simple means to export annotations, but not meant to support complete cloud sync features like Dropbox. It kinda makes sense for Reader since the device is not constantly connected to WiFi or 3G. At least that is the case works for me. My smartphone is for a constant connection.