The idea that all apps should use some kind of system style that dictates shape for every single control is... Odd. I don't know of any system that operates like this - certainly not Firefox on the Android phone I'm typing this from, nor the Windows box IT wants me to use for work, nor the Linux VM running inside that.

Especially for web apps, writing them so that they look good on every browser with default styling for every element is... Difficult.

Not to mention, users often use the same app from different browsers (laptop, phone, tablet), and are much more easily confused by the different styles of each device and browser than if the app itself is consistent, but different from other apps.

Edit to add: I'm very curious if you can find some major sites that do actually use the default checkbox controls - Google doesn't, YouTube doesn't, Apple doesn't, Wikipedia doesn't, Mozilla doesn't (though I did find a default radio button on their donate page), Microsoft doesn't. Even HN uses plenty of default controls, but still you'll see some custom controls, such as the upvote/downvote buttons.