Also, fun fact, the error occurs on Chrome but not on Firefox, due to inconsistencies in how they handle the root scrollable element.

I'm actually not sure if getClosestScrollableContainer should return the root for the body, since arguably body doesn't have a scrollable container – it is the ultimate scrollable container. But that would probably be saner than retuning null or throwing exceptions, and even our own code expects that behavior.

Change 343549 had a related patch set uploaded (by Bartosz Dziewoński):
[oojs/ui] Element: Add special case for document root in getClosestScrollableContainer

https://gerrit.wikimedia.org/r/343549

Side note… looks like the way you position the popup no longer works correctly, partially also due to that change, partially due to rGOJUa3caf97b7167: PopupWidget: Make popups able to actually pop *up*, as well as sideways. But I'm not really sure if this should be considered a regression in OOjs UI or a pre-existing bug in how you do positioning that was now exposed.

For reference, the current code is:

offset = $icon.offset();
tooltip.$element.css( {
	top: offset.top + $icon.outerHeight() + 5,
	left: offset.left + $icon.outerWidth() - 20
} ).appendTo( 'body' );
tooltip.toggleClipping( false ).toggle( true );

There are two ways you could fix it:

1. Disable the built-in positioning and position manually after you display the popup:

offset = $icon.offset();
tooltip.$element.appendTo( 'body' );
tooltip.toggle( true ).toggleClipping( false ).togglePositioning( false );
tooltip.$element.css( {
	top: offset.top + $icon.outerHeight() + 5,
	left: offset.left + $icon.outerWidth() - tooltip.$element.width() / 2
} );
tooltip.$anchor.css( 'margin-left', '50%' );

2. Instruct the popup to position itself relative to the checkbox icon:

tooltip.$element.appendTo( 'body' );
tooltip.setFloatableContainer( $icon );
tooltip.toggle( true ).toggleClipping( false );

Change 343549 merged by jenkins-bot:
[oojs/ui@master] Element: Add special case for document root in getClosestScrollableContainer

https://gerrit.wikimedia.org/r/343549

On 0.20.2 the positioning is completely broken (this is without changes in Translate):

I have to scroll down to even see it.

Same effect on ULS tooltip (T161203).

Yeah, like I wrote above (T160852#3112935), you current code conflicts with the new built-in positioning. Depending on your perspective, either your code relied on unspecified behavior of OOjs UI, or we made an accidental unaccounced breaking change. But either way, at this point it should probably be fixed in Translate – feel free to copy-paste one of the snippets I gave in my last comment.

From the OOjs UI point of view, this issue is fixed (after my patch, no exceptions are thrown). I'll split off a separate task for Translate and close this.