Dear Serif,
Please, put your users first and consider list your software on the cross-platform Steam store.
You say it's "out of your control" that you cannot provide licenses for Windows because you use the Mac App Store, so the next logical question is: why are you limiting yourself to the Mac App Store? The Mac App Store is not the only game in town, and in many cases (especially for games) it's quite foolish to purchase from there unless you like being locked into an ecosystem, where purchases are lost at the switch of a platform.
Steam has already solved this problem with the cross-platform option Steam Play, and it's available for sellers of software too. Many creative applications are already listed on the Steam store and the Affinity suite would fit right in. Sure, the Steam store has the stigma of being for gamers and game developers, and may not be the exact pro audience you're trying to cater to, but that will only change through action. Plus it's only an option in addition to places like the Mac App Store and Windows Store.
The only reason I can think of being against this is privately hoping to make purchasers buy the application twice. Since I'm guessing you aren't the type of company to behave that way, I really hope you'll earnestly consider putting your software up on Steam. It would be a huge win for consumers who use Boot Camp, people who are thinking of making a future switch to Surface (as many seem to be lately), and folk who just value their software.