And why should they count the same?
No game store charges you per download.
On gog, steam, even google play you buy a game, not a download, and when you own it you can download it as many times as you want. Try any other store and you'll see that they work the same.
If I buy a game, and I have a laptop and a desktop PC, I can download the game on each computer, one purchase, two downloads, for example.
What is a mistake, is that Itch counts you when you start downloading a game and not when a download is completed successfully. If for example, I'm having internet problems and the download fails 4 times, on Itch you'll see 5 downloads, but in reality, the game only finished downloading properly once.