Alpha Floor is an additional protection which applies TOGA thrust when the aircraft reaches a certain angle of attack threshold, again to avoid the stall. This threshold varies according to several factors, one of them being aircraft configuration. Also, when the aircraft is extremely nose high (greater than 25 degrees nose up), and the pilot pulls the sidestick more than 14 degrees back, the Alpha Floor will activate.
Alpha Floor will engage and apply TOGA thrust regardless of thrust lever postion or autothrust engagement. In other words, you can have the autothrust disengaged, and both thrust levers held fully closed, and Alpha Floor will still engage if required. You do not get Alpha Floor is when either the autothrust is unserviceable, or the aircraft is below 100ft RA in approach. There are one or two other times as well, but these are the main ones for normal operations.
The only way of getting out of Alpha Floor once in it, is to disconnect the autothrust.
I would be very surprised if CX has been getting Alpha Floor on flap retraction - you can get it, but only if you abuse the aircraft completely, and CX are not exactly renowned for abusing their aeroplanes.
Hope this helps