(Assuming zoning checks out) The additional unit would only be creating more cash for the mortgage payment so I just don't see how this could negatively affect a lender. 

See the affect of PA house Bill #352 lowering Quiet Title times via Adverse Possession to ten years for some PA residences.) https://www.legis.state.pa.us/cfdocs/legis/LI/consCheck.cfm?

She repeatedly told me that I should pay more to make the deal close.

The most affected communities are in Chester and Delaware County.

Will the HELOC affect our joint tenancy in any way? 

All of those questions are answered in David Greene's book "BRRRR: Buy, Rehab, Rent, Refinance, Repeat" To answer all of them here would be redundant, not helpful, inadequate and unorganized. 

So after all is said and done you're paying a higher rate which would greatly affect your ROI.

Our goals include providing education to our members, providing professional networking, and monitoring the political and legislative environment as it affects the real estate investment business.

I'm curious what Flippers, BRRR buyers think of it and if it will affect your business at all??

For this first investment I plan on living in and updating a single family home and then moving out and turning it into my first rental property, and then repeating.