VMs bring greater isolation but they're a lot heavier and slower. The agents just use github for synchronization here, though I've been considering building some kind of todo list overlay locally.
Early on in development I tried to harden the container to prevent deliberate escapes by the agent. This was a waste of time as the agents just kept finding more and more exploits when I asked them to try and break out.
Personally, I run yolobox directly on the host. Being able to tell the agent it has sudo and can install and do whatever it needs to accomplish any task is handy.
I made some comments about exploits in the original post [1]. Gemini was quite creative in adding git hooks to the repo that would execute on the host machine. That folder is shared.