The direct edition (available from this site) and the Mac App Store edition are very similar, but there are a few minor differences:
- The direct edition will download to your Downloads folder, so simply drag it into your Applications folder to install.
- The Mac App Store edition will be downloaded directly into the Applications folder.
- The direct edition can be updated via an in-app updater.
- The Mac App Store edition can be updated via the App Store app.
- The direct edition supports beta releases to help test new updates.
- The Mac App Store edition is not updated until the general release.
- The direct edition offers optional in-app purchases via FastSpring (or from this site).
- The Mac App Store edition offers optional in-app purchases via your Apple ID (iTunes account).
- The direct edition provides 91% of the purchase price to the developer (after FastSpring's cut).
- The Mac App Store edition provides 70% of the purchase price to the developer (after Apple's cut).
- The direct edition is not sandboxed, to enable updating, though acts with the same limitations as a sandboxed app.
- The Mac App Store edition is sandboxed, requiring extra steps to approve keyboard usage detection and install action scripts.
- The direct edition stores its data in the path "~/Library/Group Containers/6Z7QW53WB6.com.dejal.timeout/", where "~" means your home folder.
- The Mac App Store edition stores its data in the path "~/Library/Group Containers/6Z7QW53WB6.com.dejal.timeout.free/", where "~" means your home folder.
That's about it. None of the differences are all that significant, so you are welcome to use whichever edition you prefer. Downloading and updating are about as easy for each, and purchasing is similar, it just depends on whether you want to buy with your credit card or PayPal account, or your Apple ID. Of course, purchasing is optional; you can use it for free if you don't want to become a supporter.