Wrapping up on this, and as is often the case: I no longer have an environment to further test this. The problem site is now on satellite backup and cellular primary.
After changing the above settings on the main core device, I no longer had any issues with it directly. I had some minor spikes on some devices, but nothing like I was seeing before - so have been unable to truly catch it in the act, make changes, and compare. I had one device on the extreme edge of the network in question which continued to show some isolated spikes.
For my case I think the max repeaters was the biggest help to reduce the window of time taken to ingest bulk stats from interfaces. It appears that some minor packet loss on a 2+ minute process was highly likely to drop some data, and obtaining it all in shorter period may have simply reduced the probability of it hitting any packet loss.