In terms of your question. Yes, out of the box it is possible to have multiple layers of debt as well as a mid-hold refinance.
Tutorial #5 should provide a basic overview for including two layers of debt:
Since the video was recorded, Spencer has since added the option to refinance the initial debt structure. To do that, within the ‘Financing Assumptions’ section click the ‘REFI’ button. That will open up a ‘Subsequent Financing’ subsection wherein you can set the terms of the permanent financing. So my thinking is the ‘Initial Financing’ would be your bridge structure, and the ‘Subsequent Financing’ would be your permanent debt plus the subsidy piece.