My guess is that their security folks aren't convinced by the robustness of the sandbox and don't want the pain of trying to defend it, which is a pity (for them), because it just throttles their own platform and pushes people towards the web. The browser guys apparently can define a sandboxable platform: why can't Apple?
Re: custom file browsers. Yes, that's a good point. I think you can request access to whole parts of the file tree though even when sandboxed. You have to mark them as exceptions via entitlements and it's automatically granted. Because Apple see the sandbox as a way to mitigate exploits and not allow execution of untrusted code, that sort of approach works fine.