It probably depends on how you collect payment for those additional features.
For paid apps there is also a revenue sharing component (currently 15%).
However, I did find this:
Does the revenue share apply to non-Checkout processed transactions?
The revenue share applies only to Checkout transactions, that is, any charges in your Recurly account linked to your AppExchange Publishing Organization (APO).
However, I'm not a lawyer and that isn't legal advice.
Based on the AppExchange Partner Program Policies (Currently linking to ProgramYear2019, which appeared to be current when this was posted). Interpret this section as you will:
part of the ISVForce Partner Category, Partners may distribute free applications to existing SFDC
customers. Partner’s distribution of free applications to existing SFDC customers does not require Partner
to pay SFDC fees (other than Program Fees) for such distribution; provided, however, that an application is
only a free application for the purposes of these Program Policies if the applicable customer can install
and/or access and make full use of all of the features and capabilities of the application without paying
Partner fees of any kind. A Partner application that integrates to or makes use of any application, service or
other product for which Partner collects fees is not a free application. (For example, an application is not a
free application if it is provided under a “freemium” payment model or if it requires purchase of another
application from the applicable Partner.) SFDC reserves the right in its sole discretion and at any time to
determine whether an application is a free application for the purposes of these Program Policies
From my, very non-lawyerly, reading it seems like it is only a free app if there aren't fees involved for using it. That middle section seems fairly clear that you aren't a free application when you start collecting fees.
With regards to what happens when an existing free listing is converted to a paid listing I've asked for further clarification via the Partner Q&A forum.