The revenue code has nothing to do with the loan potentially being a small business loan. It's the size of the loan that matters. Once it is determined it is a small bus loan then the GAR is used to distinguish small bus loans to truly small businesses. In this case, if the loan is <=$1million and it is to a non-profit and if it is secured by non-farm non residential real estate the loan would be reported as a small business loan and the GAR would be recognized based on what was considered for the credit decision (as you state). However, if you are undergoing a CRA exam using the ISB standards you would be allowed to select on a loan by loan basis how the loan would be treated for CRA PE purposes. So you could have it counted as a CD loan even if you had to report it as a small business loan.
CRA Exam Preparation, CRA Performance Evaluations, Key Performance Benchmarks, & maps