This update you refer to is described in the following item of the App Store Review Guidelines:
4.2.6 Apps created from a commercialized template or app Generation service will be Rejected.
That is, basically are apps that are originated from templates. Apple implemented this rule to contain basically two situations:
Companies that develop and market generators of basic apps that are just a template where logos and text are exchanged.
More complex apps that are developed to suit many different customers, but the same app is cloned for each customer.
This second case generated much protest by the developers and the rule was updated to:
4.2.6 Apps created from a commercialized template or app Generation service will be Rejected unless they are submitted directly by the Provider of the app’s content. These services should not Submit apps on behalf of their clients and should Offer tools that Let their clients create customized, Innovative apps that provide Unique Customer Experiences. Another acceptable option for template providers is to create a single Binary to host all client content in an aggregated or "Picker" model, for example as a Restaurant Finder app with Separate customized Entries or pages for each client Restaurant, or as an Event app with Separate Entries for each client Event.
That is, the recommendation given by apple itself is q, or each app is published in the account of its respective customer (the content generator), or that a single app be published with login or selection of each customer.
In this article the case is well explained: https://macmagazine.com.br/2017/12/21/apple-revisa-regra-importante-da-app-store-referente-a-apps-criados-com-base-em-modelos/
And to answer your question, the fact that your app is in Ionic doesn’t exactly have to do with the rule.
Good answer. So much for Ionic that in the apple forum you find programmers who made native apps using Swift who had the same problem, in several countries. Both in apps and games.
– André Vicente