Prefer a contained project location
Keep experimental autonomous work in a dedicated repository or disposable WSL/container environment rather than giving broad access to your entire Windows user profile.
Use the same permission modes
Claude Code permission modes such as Manual, Auto and bypassPermissions are concepts independent of the operating system. The safety difference comes from what the process can reach and what credentials are present.
Watch mounted Windows drives
A WSL session may be able to reach Windows files through mounted paths. Isolation is weaker if the autonomous process can still traverse into valuable host directories.
Keep rollback easy
Commit before long-running tasks, review diffs from the Windows or WSL side you actually use, and keep production secrets out of experimental sessions.