What happens if you pad the end of a programme by say 5 min causing it to clash with another scheduled recording ?
If you mean another recording on the same channel, the HDR won't let you do that, since it won't make two recordings simultaneously from the same channel. If you mean two different channels, then it's like any other situation where you schedule two overlapping recordings. Manual padding just becomes part of the scheduled recording time.
In principle there's no problem with overlapping recordings, since the HDR has dual recording. But when the time comes to begin the second of the overlapping recordings, a problem arises if you are watching a third channel and the three channels involved are on three different transponders. In that case the HDR can't access all three channels at the same time, so it offers you the option of cancelling the second recording, so you can keep watching what you're watching. If you don't cancel a recording it will switch the channel on view to one of the channels you're recording, and the two recordings will proceed as scheduled. (This will happen automatically if you do nothing or the HDR is unattended.)
I use the auto-padding option, which automatically extends all recordings by a fixed amount. This is rather different from manual padding, since the scheduled recording times are not changed, and the HDR just extends the recording when it takes place. With auto-padding you could accidentally schedule three recordings which will overlap once padding is added, e.g. you could schedule recording of programmes at times 2000-2200, 2000-2100 and 2100-2200 on three different channels. In this situation you want to record three programmes simultaneously around 2100, to include padding. Obviously the HDR can't do that, and it often makes bad choices about what to record. It may, for example, truncate the 2000-2200 programme half way through, so that it can add padding to both the other programmes! Be wary of this if you use auto-padding. I believe the same sort of thing can happen with AR, but it's much less likely.