If there is something complicated with it, you might want to let the contractor know ahead of time. 

How do you experienced rehabbers get more complicated construction costs dialed?

It's a pretty simple, fair system that seems to be lost on many judicial districts. 

You could possibly do a "subject to" which is a slightly more complicated process.

We haven't decided if we were going to actually form the partnership officially or not since the taxes become so complicated.

It's an additional level of complication that is unnecessary but the money remains in my pocket, I get some additional tax benefits, and I know the true cost of my business and the true income of my investment in case something changes.

They do not make it easy for you and will show no mercy when writing up infractions, which are bound to happen because of how complicated they make the process. 

I usually do my own taxes, but this time I have an LLC and it's become much too complicated.

I agree with your concern of flipping at a distance as this complicates the whole process (especially when you are a new investor).

I think this type of clause can get very complicated and convoluted.