[weblacky]

My brain chocks this up to just supplier and production run.  SGI didn't make 1 million of each system. They had a dedicated production run for every PCB revision, I assume.

They sourced the parts they could, and you might expect there to be differences between generations of each production. At most a heatsink is a heatsink as long as it meets the basic requirements under testing. if your question is, could you swap the heatsinks and everyone would be OK, I would suggest no, but that could be for a myriad of reasons, including the thermal envelope of the processors, and any kind of adjusted tolerance between them. 

Given the processes we're talking about I assume that they are more efficient not less efficient than the old models. Therefore, I would assume that having a heatsink with larger fins but center material means increased airflow but less heat saturation and thermal load.

Again, that's a guess. But I think there was a fair amount of time between these two processors being put out.

Even today, it's super common that you secure parts for a single production run. After that production run, you can go back to your suppliers and try to get the same parts but likely a certain percentage of them will no longer be available or you'll have to go with a different supplier for a similar part. This is just how our world works because nearly everything is done in short-term batches with a lot of stuff not being continuously run off a production line for years and time.

A lot of times semiconductors will be around for many many years but a lot of things like passive components, heatsinks, standoffs, screws, and bolts, etc will be sourced every production run.