Historically, it's generally been cheaper and easier to have two chips than to persuade a consumer or server OS to provide reliable time guarantees.

Hypervisors like that already exist and are needed by cloud providers.

Well, even in that context you have AWS for example doing control plane operations on a different SoC - https://docs.aws.amazon.com/whitepapers/latest/security-desi...

I think it's more the fact that the M2 chip is used across multiple product lines that don't need the unique capabilities of the R1 chip.

I think it makes sense. The parts of the system that need to respond within certain time windows because of physics run in the R1 (presumably, “realtime 1”). Everything else is just an iPad, which currently runs on the M2.