I believe learning to maximize my time will lead to my FIRST DEAL, which will lead to my portfolio....

You just have to think about comfortability vs profitability. 

If it is a goal to maximize cash flow, then Company A is your answer.If the goal is to remove the liability of the property, then Company B. 

Since I am new to real estate investing and am just starting to feel comfortable analyzing SFH and SMF rental properties, I am not sure that I know all I need to know to take advantage of this deal.

I tell people to underwrite and buy their deals if the long term rental numbers make sense and to use short term rentals to MAXIMIZE their investment.

My wife and I were interested in securing an office building that met our requirements to serve as both an office and small residence to maximize the amount of cash we could invest into our business.

If you feel more comfortable or confident with an experienced manager and don't mind paying the extra fee, I don't see why not. 

If the duplex is making money comfortably and you don't see any red flags (neighborhood going downhill, area losing jobs or population, etc) I would keep it and grow your portfolio by whatever means makes sense

I'm looking for layout ideas and a design that looks a little nicer than a generic building and maximizes the limited space I have.

They usually have overinflated revenue and low expense assumptions.If you’re comfortable with the numbers on it, just keep in mind that you likely won’t be able to replicate the total rent in the “by the room” model in a traditional long term rental.