The direct edition (available from this site), the Mac App Store edition, and the Setapp edition are very similar, but there are a few minor differences:

Download

The direct edition can be downloaded from this site.

The Mac App Store edition can be downloaded from the App Store app.

The Setapp edition can be downloaded from the Setapp app.

Installation

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 Setapp edition will be downloaded directly into the Setapp subfolder within the Applications folder.

Updates

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 Setapp edition can be updated via the Setapp app.

Beta releases

The direct edition supports beta releases to help test new updates.

The Mac App Store and Setapp editions are not updated until the general release.

Purchase

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 (Apple iCloud account).

The Setapp edition doesn’t offer any purchase; all features are always available as part of your Setapp subscription.

Proceeds

The direct edition provides 91% of the purchase price to me, the developer (after FastSpring’s cut).

The Mac App Store edition provides 85% of the purchase price to the developer (after Apple’s cut).

The Setapp edition provides a portion of your Setapp subscription to the developer, based on the number of people using it each month.

Sandbox

The direct and Setapp editions are not sandboxed, to enable updating, though they act 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.

Data location

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.

The Setapp edition stores its data in the path “~/Library/Group Containers/6Z7QW53WB6.com.dejal.timeout-setapp/“, where “~” means your home folder.

Your choice

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 the direct and Mac App Store editions are 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. And if you have Setapp, it makes sense to use that edition, since it’s included in your Setapp subscription.