I think it's a reasonable question. The answer is that not everything does indeed run in a VM or a container: lots of things (notably on developer machines) run directly in a host user context, where they have access to all kinds of global state that they don't really need (developer credentials, browser state, etc.).

But also: even within a container (which isn't itself a sandbox) or a VM, you still have concentric circles of trust and/or privilege. If you're installing arbitrary dependencies from the Internet, for example, you probably want a basic initial defense of preventing those dependencies from exfiltrating your secrets at build time.