But to me as a businessman that seems like a workaround if I were personally needing to take a large dollar amount right off ahead of doing business.

If you want to install it on your own home so you can feel good/smug, go ahead, it’s your money.

4) Is there any good way to "calculate" the new appraised value ahead of time to know what to fix/rehab?

I have seen COUNTLESS people get a head of themselves on this platform.

Build a contingency budget into your plan by allocating an extra 10-20% for these surprises.To get ahead of potential problems, conduct thorough inspections from top to bottom before buying a property.

Would love to hear how you went ahead and structured this. 

Go ahead and purchase it.

So, that if they stay longer or have multiple pets I will end up ahead on average but otherwise over the long run I am reasonably protected for the additional damage risks.

You could have a few things driving the cost:-Location - if the house is more remote the contractor will have higher costs to get out there (gas, lodging, limited resources) or if you are using a local guy he might be higher because he knows there are fewer competitors -El Nino - the roofers we use are all busy because people are rushing to get work done before the rains hit.  

Work hard and you’ll be able to get ahead and will be able to find deals.