This is allowed for conforming loans, but no all lenders choose to actually take this extra step or sometimes their loan officers don't know. 

Conforming loans such as a conventional, FHA, etc are for residential customers. 

Due to the long vacancy the lose their non-conforming condition and you have to file appeals in attempts to get it, so double check this before you jump down the hole.

So, you your exit strategy, assuming its a hold, needs to be qualified before you even buy.If you are using a LLC to hold Title, then you won't be eligible for a conforming residential loan. 

Also, legal entities such as LLC's are not eligible for conforming residential loans, so you will have to use commercial financing. 

I do not want to run into an issue where I buy the home and then im unable to obtain the permits, or have to tear down the unit because it is non-conforming. 

You have to be careful since the non-conforming unit's income is not lendable (as in you cannot claim it as income for future lend-ability). 

It has been grandfathered in and currently is allowed to be an operating, non-conforming triplex.

Even if it did conform to FHA guidelines, which I don't think it does, you still have to get the bank to approve the loan.

I am contemplating doing a cash-out refinance to pull maybe 500k-600k (to keep it under conforming limits).