The IRS' preferred methodology for a study is engineering-based, done by a licensed engineer and an expert in construction.

Unless you like spending time with auditors, I highly suggest only using the IRS' preferred methodology, an "engineering-based" study.

Does this sound logical, should we follow a different methodology?

You usually don't see other investors giving away that much equity unless they're ancient and don't care or inherited the property and don't care. 

Even if units are vacant the appraiser, in complying with rules of the Appraisal Institute, will use comp rents to arrive at a likely rental rate for the vacant units, unless their is no demand for those units as rentals or the cost of getting the vacant units in condition to rent is greater than the net present value of the income stream they will produce.In any case, without going deep into methodology, MAI appraisers will determine if the demand exists for renting the vacant properties.

If we were to use existing HELOC funds, then it’s just up to how much mortgage rates change in the 6-12 months we’d have to wait to re fi.To your point, if we can do REALLY well on the BRRRR methodology, I’d rather be efficient in terms of aligning with our long term strategy, and it sounds like we might be able to do that if we choose carefully.

The notion that Dave Ramsey's advice is for the poor or middle class is a fair argument in his methodology for real estate investing but when it comes to the tried and true staying out of bad debt and sticking to a budget; he could not be more spot on for anyone. 

Bottom line isn’t whether you agree or disagree; the articles reasoning, methodology and conclusions are predetermined and biased, so the article is beyond useless.  

I followed the methodology listed in the phila.gov website here - https://www.phila.gov/services...I got the BIRT and CAL, but when I go to the last step in applying for rental license for my property.

Things have changed and even a good engineering-based cost segregation study (the IRS' preferred methodology) is much more reasonable.