Michael Tsai notes apps are already being constrained by the app store limits. This is because some APIs only work if your application is in the app store. Right now that’s primarily iCloud but it’ll almost certainly increase in the future. I’ve been calling this as a problem for a long time. It wouldn’t be an issue were some of the app store limits not so egregious. Especially in terms of sending Apple Events.
PDFpen is getting around this issue by utilizing a helper app bought via the app store. That way the main application can get around API limits or sandbox limits while the helper app utilizes app store APIs like iCloud. It’s a kludgy hack and may stop working in the future if Apple puts further sandbox limits on what files an application can access. I suspect you’ll see more kludges like this in the future.
In the meantime I’d be careful about what applications you buy through the app store. If an application accesses many files independent of a standard file dialog then do not buy it from the app store. You’ll face grief in the future. When I got BBEdit I was careful to ensure I bought it direct instead of via the app store. The two versions are not the same. The app store version has reduced functionality and will probably have much more reduced functionality when the sandbox limits become more pronounced.