Is it worth the money to have this done in my 2 family?

Is his net worth over $5 million? 

For resale in a B - A class single family residential neighborhood, definitely. 

A benefit of a USDA loan is that it has lower credit requirements, and it offers 100% financing, but there are income limits. and if you find a house in a USDA eligible area, you're going to seriously limit your market for rent and/or resale due to low population.

If he finds a deal that is getting a return higher than the debt, then it may be worth while to go for the deal.

I just haven't found it worth the trouble for the amount in security deposits I'm holding (<$10k).

Finally, is it worth it or even possible to later put this Philly house into an LLC, especially if we plan to take equity out for another property?

It seems like the "goal" ultimately boils down either to a net worth $$ amount or a passive income $$.

Then watch the auction and you will see in real time what other investors think it is worth.

@James Webb I agree with @Nicholas Aiola and also would re-iterate that it wouldn't be worth paying for a cost segregation study on a smaller property like that one.