Apart from what
@vikingar said, storage cards also tend to have firmware that is, let's call it 'optimized' for camera and phone workloads. Those firmwares are sensitive to where the file allocation table is stored (yes, most card firmwares assume a FAT based filesystem) and the offset of the partitions.
On top of that, previous Canon cameras strongly preferred a specific Canon flavour of FAT filesystems. It was still in spec, but different to how Windows and Linux tools would format it by default.
In the era of the original 7D, you should squeeze out a bit more performance by partitioning your CF card in a specific way and then reformatting it in camera. The partitioning would force a specific layout and filesystem, the reformat in camera ensured a Canon-flavoured filesystem. And extra 10Mbyte/s was very noticeable in those days!
But the most likely reason Canon support said is, is as others remarked, their way of getting you to 'turn it on and off again'. It is likely to improve things and resets it to a known good state, but I don't think it will massively decrease the heat generated. But the combined effects might drop it below a threshold that makes it much more useable to you.