The actions are placed in the order in which they have been learned onto the bar regardless of controller or keyboard.

I have yet to lose my settings either from the servers or from a local backup and have transferred via both across various systems. But then I also yet have to have my settings reset.

And it's helpful to see what was removed from the game and needs replacement.
Some of the bars I no longer use (Conjurer) have actions from the beginning of 2.0 on them right were I left them when I became a white mage, the bars survived all the time from then across several systems.