You’ve got the right idea when it comes to liability protection and separating the income for tax purposes, but there are a few things to consider with the "due on sale" clause.When it comes to paying the down payment, it’s perfectly fine to use your personal account to cover it since you’re personally guaranteeing the loan anyway.

The house and ADU are close together but separated by a 6 ft privacy fence.3. 

Not unless you have them as two separate things-they pay rent like all of the other tenants and are treated the same way and you then pay them separately for the work they do.

Therefore, amounts separated for by a cost segregation study would not technically increase the "non-real-estate-property" for the purposes of the 15% test.

I'm unable to come up with a solid solution here (adding a separate gas meter is too expensive.) 

You would be best served by managing them with two separate apps.

The most important advice is not to get emotionally attached to properties (If viewed as an investment vehicle, Owning for personally reasons is difference).

By what you have said, it sounds like you are thinking about this place as an owner (emotionally) vs a realtor (sorry if I am reading into this, but your statements about charm etc.).  

Essentially how do we separate from partnering on each property when the time comes? 

Just update that lighting to make it look warmer and you should be good to go.I would create a separate bank account for the place.