That may complicate the deal.

So, we are leaning towards buying the property via two LLCs, although I'm a little concerned that this will make things (like obtaining loans) more complicated for us in the future.

This might sounds complicated but your attorney (probate or family planning  better) or a financial advisor can advise better on this because it varies between states.

When you rent out your primary residence, your taxes become "complicated." 

As a data point for you, I underwrote and negotiated a 5 home subdivision in San Marcos last year (that I didn't end up moving forward with because of utility complications) that had a $800k land cost.The problem in this case is the land cost is too high for scraping and building. 

Doctors and nurses are up close and personal sometimes for extended periods in close proximity, touching all sorts of bodily fluids etc.   

In general the powderkeg that exists here is that your PM has a VERY complicated operation, created by the way they are structuring the business. 

The thing is that my relationship is a little complicated now but I hope it to get back to normal so I am not sure for how long am I going to stay in that condo.

In reality it’s more complicated than that.

Yes, their taxes will be a bit more complicated because they need to provide you with a 1099 every year for the interest paid.