There most certainly is a distinction between the two. Yes, there is no pre-determined FS and SS, and yes, they don't trade on motion.
But the game of football, and defensive planning is built on tendencies. Percentage laws in football tells us that right handed QBs have right handed offenses, meaning that the TE is on the right side of the formation from the offenses perspective. If most of the time, the strength is to the left (from the defense's perspective), the physically imposing would be to the TE side, and the more ballhawking Safety would be to the Right side.
The assets of the LS and RS instead of a true FS and SS, is seen in our coverage selection. Since our defense plays a lot of Cover 3 and Cover 1, you teach both safeties to be able to role in the box, play centerfield, etc. However, Saban, and any DC worth his salt, will make sure that most the time, the better ballhawk will rotate to the MOF (Middle of the Field) for Cover 3 and 1, while the more imposing safety would rotate into the box (or go man-on-man in C1).
So yes, there is no FS/SS in theory since they don't trade, but when the Sky/Cloud/Funnel/Rotational calls are made, you bet your *** that whoever calls the plays has the coverage/physical traits in mind that are traditionally seen in a FS/SS. As I have said, you have to have change-ups; you gotta switch responsibilities to avoid being predictable -- but you also have to play to your strengths. The scary part is the line is blurring and that's why Saban doesn't make an actual "distinction."
However, I bet my car that Allen will be playing more Centerfield than the other safety!
Oh well, there is my two cents...