Few different things at work here. For starters...
About unlocking via 'serial key, see ASRGs 3.1.1 In-App Purchase
>client would like it to be a native app.
Is the client aware of the risks related to ASRG 4.2 Minimum Functionality
>User are required to create a free account where they can use the free portion of the app. If they bought the book
Are you aware of the ASRGs “Reader” Apps?
>also planning to offer in app purchase
In that case, you might want to move this to the IAP forum. See FAQ4 here: For Best Results - Read the Label
>Is this compliant with the guidelines from Apple.
Pls. note there are no pre-reviews, App Review isn't here, and no one here can offer any promise, just their opinion(s) and/or the occasional confirmation of what has previously been suggested.
My opinion is that having both internal and external processes for buying books can create a risk during review, again, see “Reader” apps via the ASRGs.