These checkboxes should all be converted into toggles.
CC @tyxla to do the same in Calypso (if not done already)
Thanks for the ping, @MichaelArestad! Here is the progress of those in Calypso:
Every checkbox in the spelling and grammar advanced options (Fancy options)
We haven't started implementing these yet.
The metadata checkbox in the media section to show meta info in carousel
This PR is in progress - https://github.com/Automattic/wp-calypso/pull/10925 , cc @oskosk to verify it's done there.
The infinite scroll checkboxes (do we even need the first checkbox setting there?)
✅
The Subscriptions checkboxes
✅
The WordPress.com login checkbox.
Does that refer to the "Stay signed in" checkbox in https://wordpress.com/wp-login.php ?
@tyxla that last one (WordPress.com login checkbox) refers to these 2 (only exists in Jetpack):

Updated the checklist to include a few more.
Done in Jetpack in https://github.com/Automattic/jetpack/pull/6237 awaiting review, particularly regarding the role toggles in Stats. Due to the nature of the value saved by the role options in Stats, an array, they had to be disabled while they were toggled, because otherwise there was a race condition that would have allow the user to save erroneous values if the toggles were quickly tapped sequentially.
Due to this, maybe it would be better to leave this as checkboxes.
Closed in #6237
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Updated the checklist to include a few more.