Replying to my own question here in the event that it helps others. I called NY Dept of Revenue again with this specific question, and after some internal checking, the agent said the following:
1) NY will pay interest starting from 45 days after the amended return was filed, to the point when processing is complete and the refund is issued.
2) No interest will be given from the original due date to when the amended return was filed, nor will interest be given for any delays in refund reaching the taxpayer and deposit being made etc.
3) The above applies equally to resident and non-resident return.
