Editor 2.0.4 with Bulma 0.9.2 is using Bootstrap classnames (form-check-input etc)
Specifically when a popup editor is shown it is not correctly styled with Bulma
As well, it seems setting a className in the editor fields definition has no effect.
fields.className is applied to the field's container div rather than the input itself which is why it doesn't appear to work for you.
Is it only the checkbox that isn't styling correctly for you? Looking at the Bulma docs and code I think it just needs a checkbox class on the container, so in editor.bulma.js look for:
$('input[type=checkbox], input[type=radio]', field.node() )
.addClass( 'form-check-input' );
and replace with:
$('input[type=checkbox]', field.node() )
.addClass( 'checkbox' );
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