Hi Darren,
For the Commercial financial model, SAM assumes that debt interest payments are tax deductible, so the project with debt has a higher annual tax savings than the project with no debt. You can see that on the Cash Flow tab: The "interest payment" line item under State Income Tax and Federal Income Tax, and then the tax savings for each.
If you are running SAM on a Windows computer, you can use "Send to Excel with Equations" to copy the inputs from SAM to an Excel workbook with formulas that replicate SAM's financial calculations, which can be useful for understanding how the model works.
The attached file contains two cases, one for each of the files you sent to make it easier to compare them. You can use the Inputs Browser (File, Inputs Browser) to display a list of input variables in the two cases to see how they differ.
Best regards,
Paul.