I'd like to understand the implications of sandboxing too. It must have some large negative impact on Instapaper for Marco to care this much. What is it?
In short, sandboxing is an idea where every app lives in an isolated environment. By default an application can only access its own files, every other system resource is unavailable until the user explicitly allows the app to use it. It has impact on many apps, for instance your favorite git client won't be allowed to open the repositories you've been lately working on, just because they're located in Documents.
His complaints are entirely from the Mac user perspective. (And are complaints that I share.) Tons of great apps can't be sold via the app store unless they degrade themselves to comply.