I've seen this relaxed to 2.5X depending on location and the price of your unit. if rent is 4k a month then 2.5% is 10k a month gross that gives them 6k a month before tax to live on.. if rent is 700 a month I think it needs to go the other way  4X  that gives them 2100 a month to live on as opposed to 3X were they are living on maybe 1k a month that's a pretty precarious situation for many one flat tire and rent gets missed :)  I am not saying you are wrong in the intent to make sure there is enough living money, but in practice I have found that my cheaper units (class C) have the tenants paying a higher percentage of their income to rent and they simply live on not much money.My B class properties can get tenants easily at 3X the monthly rent (start at ~$2.5K (3 BR) and go up to ~$4K (3 BR)). 

I think you could take practically any industry and play out a scenario in which this will have a major effect on that industry and it's employees. 

I feel they are over reaching and out of step with modern STR practices.

You're doing the right thing by getting practice in, analyzing deals, and building your network.

What are the best practices and methods to protect yourself as a landlord?

The new document https://www.hud.gov/sites/dfiles/PA/documents/HUDAsstAnimalNC1-28-2020.pdf spells out best practices for property managers and landlords with respect to assistance animal requests.I hope this will provide you with more info on how to determine if the animal is qualified and how to screen tenants Cheers, Yuriy 

What is best practice for dealing appropriately with tenants?

The principle holds that 10,000 hours of "deliberate practice" are needed to become world-class in any field.

But practically, it is very doubtful it would be with it to try and force the sale....could be months and many thousands in legal fees to get in front of a judge. 

I practiced law for twenty years in the U.S.