The '16bit' is describing the processor, it doesn't have anything to do with the size of your maps. You can have a 4-bit processor using a 32x32 map. You can have a 8-bit processor do 16-bit math.
The limitation of the RT is two part- your pretty much restricted to working how the stock ECU works. So that means running a MAF, using a distributor, etc. You could band-aid around this, but really if those limitations are a problem your better off just getting a stand-alone. The other limitation is the stock ECU has tons of 'features' that aren't documented. Really, even the B13 ECU has about 50 maps, and I only know what about half of them do. I learn something new on a regular basis. A stand-alone is (or at least should be) well documented.