This is such a grey area and everyone I ask says, "oh, don't worry about it. This is Philly" which is kind of nerve racking. For this reason I've only been looking at multifamilies with RM1 zoning.
Below I've included a link to the Philadelphia Zoning Quick Reference Guide:
http://www.phila.gov/CityPlanning/projectreviews/P...
In the CMX section you'll see the minimum square footage requirements that are needed to make a unit legal. However, they all have the first floor of the property as commercial. As for the rental license, I've looked up several Landlord-Tenant case dockets in the municipal courts and all you do is sign an affidavit of how many units you're renting so I've seen properties with the aforementioned zoning having been issued licenses for each unit. Also, if you are looking to finance the property it can't be done with Fannie Mae/Freddie Mac conventional terms. Regardless of its use, you'd have to finance under commercial terms.
If you want to dig deeper, you can also look up all archived documents that pertain to zoning to see if a certain use has been approved or not here:
http://www.phila.gov/zoningarchive/