Not certain, but I believe that set cpu temps are battery temps...unless the kernel has built in temp monitoring.
Honestly...the only use for set cpu on the nex as of now is overclock (which in my opinion doesnt need it), undervolt. Profiles have become pretty much a thing of the past. They used to be pretty important on the D1 mainly because that phone was clocked at 500mhz stock...and a lot of folks were clocking it at 1+ghz....so of course it would overheat.
There shouldnt be any heat probs on the nex. Ive plugged mine into mhl/hdmi converter which charges at the same time....stream a movie I rented in HD off of the android market to my TV....no skips (as long as others in the house arent sucking my wifi router at home lol)....streamed flawlessy. Phone got warm to the touch...I didnt bother with it...just let it stream. The D1 wouldve probably melted or skipped every 10 seconds. lol.
Typically the electronics are rated for ~170 deg F. so...you should be okay.
In my opinion having the set cpu service running all the time (using battery and resources) is not worth the "benefit" of undervolting or overclocking.
I think some folks just like to piddle and tinker.