But if we purchase as individuals, how do we keep accounting separate from our personal finances?

Once you buy a property in the LLC make sure you separate your personal endeavors from your business.goodluck 

Having a separate bath was viewed as a convenience, particularly for the help. 

If that price point does not get you into multifamily, I'd recommend finding a single-family home that you can convert to a duplex with separate entrances or try a rent by the room strategy.

Whatever you do, maintain separate bank accounts for the business and set aside reserves for repairs and updates.

The phrase 3rd party is attempting to denote a separation between the website and a lender is it not?    

I am newly separated from my partner and starting out in real estate investing as a single mom with low 1099 income and few assets.

Mainly fire barriers, and extra insulation in between the floors. you could go with permits for the work that is being done if you want to avoid any concerns, but as far as the city will be concerned your home is just a single family that has a Mother-in-Law suite, and you are renting the spaces separately.

I will continue in my current W2 job for at least two more years, and that job ties to a separate 401k. 

When using the landlord app I'm unsure how to use for (eventually) multiple properties that will also be in their own separate LLC.