I would consider pulling both heatsinks and checking for proper thermal paste/pad bonding.
As someone who has worked extensively with Unisys and other onsite repair techs (including in-house techs for several major "appliance" vendors you find in most large server rooms), I would not be surprised if the Intel system, upon repair, never had the CPU thermal interface material changed or even changed properly. The evidence of the digilgence in repair is pretty obvious from the way that the cables inside the system are no longer cable tied together at the proper assembly points.
Also if you were to put the same HD in each system, how do you think that would affect noise/temperature levels?
Interesting observations. Made me open both up and take another look.
Firstly, the cables on the repaired system are
strapped together. Maybe not quite as tightly as in the other system, but close enough. I don't see that there would be any airflow or other functional differences between the two systems due to messy wiring.
Secondly, the Intel HS is a bolt-through type, with the bolts going right in from the top. All 4 bolts were secured all the way, and when I removed the HS, there was a decent layer of TIM between. Slightly sloppy but not excessive. I think the HSF was doing its job fine, and as I mentioned in the review, there was nothing untoward in system behavior even during prolonged CPU stress loading.
Thirdly, I repeated several times that the HDD-related acoustics were just the luck of the draw, and certainly if the HDDs had been swapped, the noise advantage would be with the Intel system. Generally, you cannot specify which model/make drive you want with most systems from big brands -- you can only specify capacity and speed.
Finally, there was no real thermal advantage in either system; both were perfectly fine. All we're really seeing is different thermal diodes reporting on different devices via different motherboards, there's nothing significant we can conclude from the comparison, thermally speaking.