And the truth is, if the investment property was completely passive and you had zero connection with it, such as an arbitrary stock in a mutual fund, then I would agree not to get emotionally attached to any one investment.  

That means making calculated numbers based decisions, not emotional ones.

One more tip – people remember stories that trigger their emotions.

All normal emotions for going through the tedious construction process. 

I completely agree with the advice and I'm perfectly okay with not charging him rent.My concern is that by treating this property differently from all the other units in the Series LLC, I may be opening myself up to a situation where I'm weakening my LLC protections even if I keep the financials separate and in order.

There is also an emotional side to owning a rental that landlords are subjected to.

Once someone has paid, what to them is a good deal of money, and invested a good deal of time, and become emotionally involved with a particular mentor and his program, they’ll fight like hell to defend it.  

Leave out the emotion, the lies, the manipulation, etc.

Having a strong understanding of your "walk away" price (maximum you're willing to pay) gives you leverage and prevents emotional decisions. 

Look at the capital call the same way and take your emotions out of it.