Instance areas are easily monitored, and it is actually pretty insignificant for the client to sum up some experience data and load it back to a data collection server on exit. There most assuredly server side code which monitors instance data ins and outs.
That said, if Bioware says it is 5% (I have not read that but assume its true) then within the broad contact of the player base, that is probably right. The question is is that talking about only warzones, or all instances spaces. Also there is two types of lag, client lag would not always be their problem. So they could be excluding issues beyond their control.
Anyone here that thinks bioware is running this from the seat of their pants without solid metrics on a broad range of variables just does not understand big dollar business. None of that of course, helps those that are experiencing it.