I have a problem which consists of 4 processes:
i) mol1 -> mol2 (exchanges sites 1-1 to 2-1 and 1-2 to 2-2 while 3-1 and 3-2 remain the same)
ii) mol2 -> mol1
iii) mol2 -> mol3
iv) mol3 -> mol2.

I cannot define the system like this in the exchange window. It looks like it accepts just one rate for both the direct and the reverse processes, which means that it is limited to exchange between equally populated sites.

This is not quite correct. In gNMR you specify RATES, not RATE CONSTANTS. By definition, at equilibrium the forward and backward RATES are equal for each reaction. Therefore, gNMR assumes these are equal and only lets you specify a single number for them.

Thus it is only necessary to specify a single rate, but in addition of course the CONCENTRATIONS of the individual molecules are needed (define them in the Settings|Molecule dialogue) to let gNMR arrive at the correct RATE CONSTANTS for each forward and backward reaction.

This way of handling things does NOT impose restrictions on the combinations of reactions gNMR can handle, although it might be a slightly different way of specifying the reactions than you are used to.