SyncAlign includes several methods and techniques to guarantee absolute data alignment with regard to time and channels. No RME digital audio card will ever swap channels, not in stereo nor in multi channel mode, regardless what you do with the card and the signals it gets. SyncAlign also controls the timing among the channels, no matter how much are used, they will always start sample-aligned.
When the record while play mode is activated, the corresponding software first starts record and then playback (or playback then record.) SyncAlign can compensate the time difference so that an exact simultaneous start of record and playback in the record while play mode is guaranteed. In asynchronous mode (different programs use different stereo devices of one card) this part of SyncAlign is automatically deactivated.