I will share my understanding. While ver12 and ver13 share the basic file format of *.fmp12 there are functional differences.
FMPro12 could host Instant Web Publishing from a regular version. As well as for hosting FMGo for an iPad user. Doing this might work for a business that has low demands on the database access. The number of concurrent users accessing was low, then the FMPro Server 12 had to be used.
FMPro13 has moved to Web Direct to replace Instant Web Publishing. This can only be hosted from FMPro Server13. The benefit is that more than the Classic layout them can be used now.
There are now different methods to have the software, different options.