This is not a great substitute for installing through an app store because the app will not update automatically.
This is, however, a great thing to have.
A better substitute would be using F-Droid. By the way, some free software apps are not gratis on the Play Store but are on F-Droid.
It can still be confusing to manage two app stores for some people, while installing an app from a downloaded executable is usual on Windows, so Krita probably did the right thing.
What you say echoes my experience, I see a lot of apps on the Play store say "pay 1.99 here or get it for free on F-Droid", which is fair. I usually even pay the money even though I have F-Droid installed, just to support the dev.
Good question: why is Krita not on F-Droid? Probably a matter of time and effort, not a technical reason. I guess they sensibly got into the most visible marketplaces first.
This is, however, a great thing to have.
A better substitute would be using F-Droid. By the way, some free software apps are not gratis on the Play Store but are on F-Droid.
It can still be confusing to manage two app stores for some people, while installing an app from a downloaded executable is usual on Windows, so Krita probably did the right thing.