Exactly. And even if you could measure the chip below the heatsink, you'd be measuring the surface temperature of the package, not the internal temp. I wouldnt expect a big difference (like when measuring the heatsink), but nothing will beat the precision of the internal sensors. IR is a somewhat useful alternative if you have a card which doesnt allow sensor measurement of certain chips, like VRMs, and will give you an idea, but its a silly substitute if you do have such sensors.
Anyway, the mystery of my 5850 has been solved. It died. It got ridiculously sensitive to voltage adjustment, just increasing or decreasing the vcore by 0.01v made like 5C difference, as if the heatsink wasnt mounted properly (it was). Soon after I started getting artifacting, blue screens and now it no longer boots. I suspect electromigration from accidentally pushing 1.65v through it because of a GPU-Z/everest bug killed it and no amount of aftermarket coolers was going to save it. I tried baking it in a over too btw, but no dice. Its dead.
Anyway, the mystery of my 5850 has been solved. It died. It got ridiculously sensitive to voltage adjustment, just increasing or decreasing the vcore by 0.01v made like 5C difference, as if the heatsink wasnt mounted properly (it was). Soon after I started getting artifacting, blue screens and now it no longer boots. I suspect electromigration from accidentally pushing 1.65v through it because of a GPU-Z/everest bug killed it and no amount of aftermarket coolers was going to save it. I tried baking it in a over too btw, but no dice. Its dead.
Unlucky man, its a sad day for miners when one of these great cards die. Maybe it was them heatpipes not doing there job. There few about these days also
New 7800's soon which i think will go down in price when the 7900 series is released next year. I dont see the 7900 being a better miner than the 7800 series due to the new architechre. Lets hope the 7800 becomes the 8800 and so on if my suspicions are correct about the new design 
As for them IR, the better you buy, the better tyou get. All i can say. And if your unsure, Add 5-10 degrees, dependant on your 'cautiousness'. I got handheld thing used by mechcanics and its shows hotter than GPU-Z. I know what i believe. IR is 36 degrees bob on everytime in my ear.
That is just at Core 880 taking it slow as that is a lot of thermal energy to dissipate.