I ran into this, with a pcb design where the physical ffc connector was flipped/reversed to the desired orientation. The solution was to just buy the corresponding ffc. Eg. If the connector was all upper pins active, then get the one with all lower pins active.
So it kind of doesn't matter, and one can cover the cases with part selection. There are also connectors with both upper and lower pins active. The difficultly is an accidental mistake, and if the flex is inserted upside down, it will put unwanted voltages on all device pins. So they should probably be avoided.