-If you are on a private sewer treatment system this most likely will hinder adding units. 

A run down shack with old cars on the front dead lawn are going to hinder your value!

I read that it might hinder me from getting a loan.

So while it adds some additional protections, it might also hinder your ability to raise rents, etc. 

Typically, selling your property with tenants in place that aren't great tenants will only hinder your ability to sell.

But as @Kerry Baird suggests it does affect your dti which could hinder your loan applications.

My question is, How should I structure a formal partnership so that I am making my partners investment worth it while at the same time not hindering my NOI for the duration of the mortgage?

Also I'm wondering if I leave the brokerage would that hinder me from being able to purchase deals through the MLS and getting commission for it for being the buyer who is representing myself?

Depending on their response, this could greatly hinder your plan.  

Unfortunately I am hindered since I just got a new job 5 months ago and I prefer to leverage my FHA 3.5% down rather than put 15% conventional.