Apple has a habit of rejecting apps which they consider to be books and suggest submitting these kind of apps to their iBook store instead. Since I built an app with this problem using PhoneGap Build, I was wondering is it possible to submit a PhoneGap Build project to the iBook store and if so, how does one go about doing this? I've found very little information about this online.
No, it's not possible. PhoneGap is used to build iOS applications for the App Store -- iBooks doesn't support a UIWebView (or WKWebView), which is the main entrance to a PhoneGap application. You can build some HTML widgets for use in iBooks Author, but that's as far as you can go.