Do the contacts interfaces with two separate inputs (20490,14490,16940) allow configuration of the two inputs to two different SAI zones?

No, the two inputs must be configured to the same area. You can for example connect a sensor to input-1 for technical alarms (setting the appropriate parameter as per instructions) and a magnetic contact to input 2, but both will be associated to the same SAI zone. You can instead choose to configure the two inputs to areas in the home automation menu that are totally different (each is configurable to a maximum of 4 home automation zones + 1 SAI zone): A common example is connecting a roller shutter to input 1, and a magnetic contact on the same window to input 2 in order to protect the shutters and window when the SAI is armed, but also automatically arrest room heating if the window is opened when the SAI is disabled (therefore setting input-2 in the relative climate zone).