I may not be correct, but this is the way that I understand things.
The time out timer on a repeater is affected by the input signal. In other words, it will time out if a carrier is detected on the input side of things for x amount of time. So if a repeater emits a roger beep to let everyone know that the person that was talking has now stopped, that also tells the repeater that it no longer recognizes a carrier signal coming in on the input side. If following the beep is a 5 second squelch tail, that's the repeater transmitting without a carrier present on the input side. Does that make sense?
If all of that is correct, a repeater set with a roger beep followed by a 5 second squelch tail shouldn't time out unless someone is long winded beyond the specified time.