This is what Apple have written back:
Guideline 3.1.1 - Business - Payments - In-App Purchase
Your app or metadata includes an account registration feature, which is considered an access to external mechanisms for purchases or subscriptions to be used in the app. Specifically, your app description contains a link to your website where users can register.
This is what they said to resolve the issue:
To resolve this issue, please remove the account registration feature and any other fully qualified links to your site that could indirectly provide access to these mechanisms, such as links to web pages for support, FAQs, product or program details, etc.
The app I'm developing is a B2B app where in a company can buy a subscription via the website and register its employees as users. What Apple is saying is that this is considered an external mechanism and that you should only use in-app purchases. The thing is that even if in-app purchase is implemented, because it is a B2B app and not a B2C, not every user has to buy a subscription, only a company has to buy one. It would help knowing if someone has gone through similar issues and what it took to resolve them.