Once you enable MFA for a RADIUS client using the NPS extension, all authentications for this client are required to perform MFA. If you want to enable MFA for some RADIUS clients but not others, you can configure two NPS servers and install the extension on only one of them.
Configure RADIUS clients that you want to require MFA to send requests to the NPS server configured with the extension, and other RADIUS clients to the NPS server not configured with the extension.