Thank you for considering iThoughtsX. There are 3 ways you can get a license - either via the Mac App Store, the SETAPP subscription service or by purchasing directly from this website. There are benefits to be had either way (depending upon your perspective.)
Convenient, central app admin.
Can use iTunes gift cards.
Subscription pricing - with access to many more top tier apps included.
Bug fixes and new features will be available here first.
Accepts PayPal
Discounts are possible (volume, education etc.)
More money goes direct to the developer :-)
Is it obvious which one I prefer?
A few other points worth considering:
Functionality-wise, the apps are identical
All apps support iCloud 'syncing'.
Purchasing direct from this website is safe, secure and handled by Fastspring.com (as used by Adobe, Smith Micro and Smile-TextExpander amongst others.)
Updates to the app are handled automatically regardless of the way it is purchased.
All license schemes allow the app to be installed on multiple computers (so long as only one person is using it at any one time.)
Whichever way you choose, I'd recommend that you download the 14 day free trial first to ensure that the app meets your needs. If you have any questions, let me know.