She is willing to try to rent the apartment, but wants to use her pre-paid last months rent (we required at time of renting due to questionable credit.) for January 2020 rent.  

For example get a credit card even if prepaid, get a loan and pay back, and also find someone with a high credit limit cc, that pays it off monthly, and that the credit card is more than 3 years old and have them make you an authorized signer-it will give you years of excellent credit on your credit report.

When using the BRRRR calculator, is it best practice to include prepaid homeowners insurance and prepaid property taxes paid at closing in the 'Purchase Closing Cost' section?  

Not sure what you mean by last month's rent but if you mean a prepayment for last month's rent, then you can create an invoice for it using an item mapped to Prepaid Rent Liability account.

The only thing that usually happens to change costs or terms is that the rate isn't locked or pre-paids were miscalculated. 

Could certainly be possible on larger dollar assets or my free and clears where my net cost excluding pre-paids is closer to 2.8% 👍 

Most of these items were prepaid in the lead contract but need to get finalized.

Any pre paid/upfront fees?

@Lucas Carl and @EJ Hulse -   max seller paid closing costs/prepaids/concessions are as follows - and not exactly dependent on a market (I'll explain this in a moment), they are dependent on loan type. 

You can get Title Costs quoted to you from your Title Company which include Title Insurance plus their other Title Costs BUT the prepaids can vary dramatically depending on the following:1-The Type Loan you are getting.