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. 

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. 

So you have all those things going for you compared to not using an IRA.Don’t put a tax advantage investment inside a tax advantage account or over complicate the entire thing. 

I would just flip where I live it’s hard enough when you can go look at the property every day What makes you want to add another level of complication and expense?