When you choose two or several different orientations in the "Orientation" parameters, you will have, in the system definition, the opportunity of defining a sub-array with a "Mixed #1 and #2" orientation.
The mixed array allows the definition of strings in both orientations, connected to the same inverter.
During the simulation the I/V characteristics of strings in both orientations will be mixed. PVsyst accounts for the mismatch loss, which is the difference between the MPP of both sub-fields independently, and the MPP of the mixed I/V characteristics.
When mixing I/V curves of strings with comparable voltages (i.e. same number of modules in serie), the mismatch is very low.
However when putting modules of a same string in 2 different orientations leads to a the mismatch in current (due to different irradiances), which may be very important. This would be a very bad system and PVsyst doesn't allow it. This configuration would only be acceptable when using optimizers performing MPPT at the module level, but this is not yet implemented in PVsyst.
NB: In the version 5, you can define only 2 different orientations in a given system (option "Heterognous orientation"), and 3 different kinds of sub-arrays: Orient#1, Orient#2 and #Mixed (for both orientation on the same inverter). If you have more orientations you should define different sub-systems and perform different simulations.