Also, does isolation of a private GH instance from the public instances not provide some degree of added reliability considering the potential for DDOS or simply extreme load?
I absolutely grant you the IT infrastructure concerns. BUT Amazon is our vendor on that. GitHub provides the software. It's not like I'd be standing up a new series of physical hosts to run an on-prem GitHub built from source and managing all of the hell around that. This would be simply putting a GH-provided image on a EC2 instance and making sure we have frequent snapshots.
You should be well aware that actual architecture of GitHub Enterprise isn't truly highly available (1 active and 1 or more standby instances) unless you are a huge customer to support clustering mode. Which means you likely need to take downtime to implement upgrades since they typically require rebooting the VM.
Unfortunately anecdotal experience here is spotty. Services I run for my team are several 9's higher in terms of actual availability (note: I did not say "uptime"); and contrarily other internal services at my company have many times less reliability than services like github.
Given that people prefer external hosting for the reasons I mentioned, for many I think pulling it in-house is unappealing.