I have a thermal probe mounted next to my cpu in the manner you described; its not 'accurate' but onto itself, its not too bad. My resolution is low, however; but if you're talking about what should be a huge difference then its fairly acceptable way to do things. One thing i have learnt from here (as said above, and personal experience) no two set ups are comparable. Theres too many variables.
Granted, my set up is external (flat test bed, no case etc) with little air flow though, and I have epoxied and taped the sensor onto the cpu with thermal paste too. Theres very little external interference with the probe, barr perhaps mosfet heat. My temps seem to line up with what graphs i have seen around here; sure, I dont expect them to be accurate, persay, but relative to an extent. I'm only looking at delta T's at this stage anyway. If I had the money to spend, I'd be buying the set up that Phaetus recommended to me, but at the moment, this will do.
I guess its how far you want to take it... the better question is, whats your ambient temps? water temps? what temps do you expect to be getting?
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