Mark:
I missed your follow-up while at work today. Good thing, I decided to check up after dinner. Anyway let me see if I have any input on your questions.
Remember that I am not a residential lender, so my opinions are not really the best on this subject. Is there any advantage to getting the larger loan, or would we be better off adding some cash? The advantage of getting the larger loan is that you will end up with a cushion of $100,000 in your pocket. If you lose your big tenant or the new tenants do not materialize, you might need this reserve to keep current. The advantage of adding some cash is obvious, you will not have to pay $5,250 per annum on the $100,000 if you decide to decrease the loan amount by that much.
Should we consider the interest only loan and just make additional payments each month?
Is there some sort of pre-payment penalty on the interest only loan? I guess it comes down to an issue of control. If you can add the principal amount every month on your own, I would say that the interest only makes more sense.
What are the full terms of each option?
Is option 1 amortized over 20 years? 30 years? How about option #2, is it the same length as option #1? If option #2 is the same length then you will have to amortize the $500,000 over a shorter period. Take that into consideration as it will affect your cash-flow in ten years.
Since the new commercial property will be immediately paid off, would we be able to use it for collateral for future loans, or is our debt on the existing house the main loan consideration? Yes, you can use the now free and clear rental property as the cornerstone to build a real estate empire

If for example the debt coverage used for the refinancing of your residence is based solely on your regular income. A case can be made that the operating cash flow from the rental property is available to support another facility.
some closing observations:a- I try to stay away from variable rates, but at least this refinancing lets you lock them for ten years.
b- What is the pricing on your current mortgage? Is the balance significant? Remember that your whole loan amount will be subject to the new 5.25% rate.
c- I encourage you again to go over what I said in the earlier post about how profitable the property is.
Good luck, it seems like you are going about this correctly.