BJL,
I recall your mentioning this before. Are you implying there's a little man inside the camera that thinks, 'bugger, he's got the wrong exposure again. I'll go easy on the amplification'?
I haven't noticed that high ISO's have a tendency to clip less with overexposure, in RAW mode. But maybe you are right.
Mainly I am implying that at higher ISO setting, the amount of light reaching the photsites is less (higher exposure index, meaning a shorter exposure time for the same f-stop). Higher ISO settings entail a higher amplification factor in the charge-to-voltage conversion pre-amplifier, used to convert electron counts from photosites into input voltages for the A/D converter.
As far as I know (Jonathan might know in more detail), highlight clipping can have at least three causes, or which only the first is naturally avoided by using higher exposure index ("ISO")
1) over-full electron wells
2) maxed out pre-amplifier or A/D converter
3) at JPEG conversion
Every doubling of ISO above the minimum halves the electron count produced at wells, but then every stop of + compensation has the opposite effect. The electron count from the wells is then amplified (on-chip pre-amplifier with Canon CMOS) before going into the A/D converter, so that, with no exposure compensation, any ISO setting will produce the same signal strength going from the pre-amplifier into the A/D convertor. So it is possibe that at this stage, the extra amplification used at higher ISO causes pre-amplifier "clipping", or exceeds the maximum input level that the A/D converter can handle.
Finaly, if you use "straight" conversion from RAW to JPEG, whether in-camera or on-computer, the highest output levels might get clipped or compressed. JPEG tends to allow for only about 2 1/2 stops from mid-tone to "level 255", whereas th ndstruy standard for DLSR sensor base ISO speed measurement is placing mid-tones at 18% and the full well capacity at 170%, a bit over three stops of headroom.
If so, lowering the contrast setting (applied during JPEG conversion) could salvage something.