>>higher “good” HDL cholesterol on the keto diet

I'd be cautious around defining HDL as 'good'. It seems to be an indicator of lower cardiac events, but manipulating it does not seem to do that. For example, HDL can be raised by taking Niacin (B3) but it doesn't change mortality rates.

So, is keto changing that underlying system (whatever it is) or just changing the indicator?

I'm not a bio pro, but I've dug into the lipids system a bit - the upshot is that LDL seems to be fairly well understood, and HDL is not.

IMO, it's fascinating. If you can get podcasts, I'd very much recommend the interviews Dr. Peter Attia has with Dr. Thomas Dayspring (AKA Dr. Lipids). If you’re looking for a quick 101 on the system, check Understanding the Entire Lipid profile at Dr Dayspring’s site.