Freighter versions often have higher "Zero Fuel Weights" and maximum landing weights - makes a big difference in what you can carry. Passenger versions typically have lower Zero Fuel Weights - the maximum internal weight allowed, the rest of the weight up to maximum takeoff weight must all be fuel.
Consequently. a freighter might be able to take off with lots of internal weight and less fuel, still land without being required to burn a lot of fuel, etc - much more flexible. Jet pax and cargo planes are really affected by these factors because they carry a lot of fuel, and need to burn a lot between maximum takeoff weight and maximum landing weight.
A good way to get smart on all this is to look at different airplanes by searching the web for a certain plane and see if you can find:
-zero fuel weight
-maximum ramp (max taxi) weight
-max takeoff weight (slightly less than max ramp weight)
-maximum landing weight
You also must remember that a 747-400 or 747-400F (for instance) can come with three different manufacturer's engines - GE, P&W and Rolls Royce; and, within those manufacturers, different versions of the same basic engine. Usually the total thrust difference across all these combinations may only be 4000 lbs thrust per engine, but it does change some weight limits in some cases.
It is not unusual to find some differences in these numbers given by different sources; this is usually do to the fact that the reference source is using data for a version upgrade of some type or other; there are MANY of these upgrades on many types of airplanes in use today.
In spite of all this, a pax or freighter version with the same total thrust and similar weight will handle pretty much the same way, and have the same or similar airspeed limits such as max Mach number, best cruise speed, stall speeds, etc.
The FAA certifies these design limits - it's not the builder or user who makes the decisions.