It's because the file has an extra cost. When you claim a game on itch.io I'm pretty sure you only get the files at the base cost of the game ignoring sales. Since the standalone version normally costs 1$ more than the base price of 0$ it's not included in your personal download page.
But, as you found, once the game in claimed if you then use the buying button again you go to a generic download page where the sale price is applied to all the stuff and you can, for example, download the standalone version.
At least that's been my experience on the website.