Just an update for anybody who may be pursuing a similar path. I opened a support ticket posing the above question and the answers were;
1. No, there is no way to specify the type of interface monitoring of interfaces discovered during the Sonar discovery process. I will be adding a feature request this with more detail and additional features and will post the link here when done.
2. Short answer, no. There is a way this can be done but not without risking data corruption in the database. Since I was adding 10,000 additional interfaces the safest option was to add them manually which is what I done in the end.