Intel's stock coolers are not bad coolers at all. They just limit OC'ing and when at their max temps get very loud. But a stock cooler should be able to keep an e7500 under 65c provided the vcore is low enough for that chip. Of all my rigs liquid or air cooled, one of my quietest is my HTPC and its a stock intel cooler on a little e2180 OC'ed at 3.6GHz (at stock voltage). Keeps it at a nice 55c-60c but at medium speed. Drops to low 50's on max speed but the noise is really loud. So yes, that little round contact point on their stock cooler is able to get the job done and do it quite well. But when you have a chip that needs a higher vcore, then you turn to aftermarket coolers.

As for the cores being as much as 10c off from each other, yes. I've seen many a forum post (maybe a dozen or more), over the years on that exact problem. Seach over at OCF and you'll find a few. But in all, its pretty rare. No common reason is ever given other than the generic "every chip is different", but I'd hazard a guess at it being due to the way the IHS installed. When its placed on top of the cores, its done with a low melting point solder and under pressure. If the pressure was not equal when it was placed on, it could have left a thin game in the solder between part of the core and the IHS. This can case the part of the chip under that gap to be far less effecient in heat transfer to the IHS and you end up with crazy numbers like that. Again, just a theory I've had for a few years on this exact problem when ever I see it. No way to really tell as you would have to re-melt the solder to pull the IHS off and that would destory the gap by causing it to fill itself back in.

Now the OP could always pop the IHS off and go back to his stock cooler, but its simply not worth a the risk of a cracked core when he can get by with those temps just fine.