As long as the program is able to read the CD correctly, there is no difference. Problem is, how do you know it was read correctly? For reliability's sake, a good ripping program should read the disk multiple times. EAC does this with secure mode. If you look at the log it produces, there's a value for "track quality". If it's less than 100%, there were differences in the passes. EAC makes sure to correct these by doing additional passes and comparing. There are also certain features of the CD drive that the program should disable or shouldn't rely on. For example, audio caching. This makes reading the disk multiple times useless, because when you read the disk again, the drive just returns data from the cache, so you don't know whether the sector was actually bad.
Further confirmation is possible by comparing your rip with others'. EAC does this by looking up checksums from the AccurateRip database.