Again I have not used either of these loans myself but did read about them in Brandon's book and was rather intrigued about the different loans out there through conventional lending institutions.

There is no institution watching me to make sure I am in line-I have to take the initiative to reach out for the advice. 

Those funds are going to be more institutional.

Also, depending on what sort of entity/institution you're referring to with 'commercial lender,' some commercial lenders have high minimum loan amounts, which usually doesn't fit a fix and flip or rehab to hold deal. 

Or potentially a different lending institution that uses a different appraiser.

.- Lender (the institution, not your mortgage gal/guy) can pay.

@Jonathan JohnsonI know of no lending institution that will finance a property, other than maybe a SFR under a Govt guarantee, without the borrower having his own money at risk.It used to be known as the second mortgage crank; the buyer either ends up with no down payment or even put money in his pocket at closing.

It is one of the oldest instruments around and institutional lenders will recognize it as a form of ownership and allow you to refinance out of it.To protect from all the very valid concerns that @Steve Vaughan expressed, definitely run it through an escrow service.The primary risk is that you could be evicted like a tenant instead of foreclosed on like a borrower.  

For e.g. you might be a great contractor but your partner might be great in dealing with accounting and financial institutions.

If this is a conventional loan I doubt it will be allowed but an institutional or private lender should be more flexible (and more expensive).