Braking from motorway speeds to a standstill wouldn't put in anywhere near enough temperature to cause pad transfer, you're talking about needing 600C plus before that kind of thing happens.
All discs have a level of DTV and judder as new, this will deteriorate over time through temperature cycling or in some cases pad transfer. This is normal though and should only be noticeable to the driver in extreme cases.
The reason a driver can feel it is usually because a small amount of run-out or DTV has built up and old or worn out bushes are no longer capable of isolating the vibration from the driver. Replacing the bushes will fix it unless the run-out/DTV is really bad, changing the discs will fix it temporarily, until that small amount of runout/DTV has built up again. The usual culprit is the FLCA rear bush, (or the equivalent depending on suspension architecture).
'Re-bedding' the brakes as BMMiniparts mentioned will temporarily reduce the DTV, but it will eventually come back.