Many websites don't offer video players with the download option
why are there so few websites using the native
Because video sharing is expensive and allowing people to download would cost more. YT wants to control the video experience, so they can inject ads etc.
Advertising. It is much harder to inject custom, "targeted", ads when a user simply downloads the video (the ad's would have to be injected into the video, during the download, to allow for targeted ads).
Meanwhile, playing in the browser allows the surrounding space not used by the video to be filled with ever changing targeted ads.
There are browser extensions that allow you to download these types of videos, that aren't native