I assume that "back up this credit ... in case the card was lost." means that details of how much money is credited to each card is saved on a computer somewhere ("backed up"), so that the student won't lose the credit if he loses the card. "Use data" is not very clear to me. I suppose it means that rather than needing the physical card, the system can use the account data that has been backed up.
The text does not explain what the student has to do to activate this "backing up" and "using data", or what is done automatically by the system, so I don't think it is possible to answer your second question just from the information given.
"The bottom line? Saving money more than security per se." means that, in the final analysis, the university's motivation for installing this system was more about saving money than improving security -- even though (as I understand it), improved security is supposed to be one of the key features of the system.