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I don't think it is possible to switch default apps that way in an easy way. I think you will have resort to starting koreader from the Applications tab and the system reader from the Library tab. I also don't know if koreader uses the system database to keep track of where you are in the ebook. If it doesn't, then reading in one app won't update the other with the new position.
You use the system/config/extensions.cfg file to specify which application is used to open each type of ebook within the Library tab. However, once you open an ebook with one application, that gets stored in the database and the same application is used to open it the next time. So, even modifying the extensions.cfg file on every reboot won't alternate the reading application for a particular ebook. You would have to modify the database, as well. On top of that, if the current page is saved in different places for koreader and the system reader app, then it won't be easy to switch between them without losing your place in the ebook.
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