On page-margin boxes, the ‘vertical-align’ property behaves as specified for table cells. It always performs alignment in the vertical dimension, regardless of writing mode.
(https://www.w3.org/TR/css3-page/#page-properties)

The vertical-align property on page margin-boxes allows to manage the vertical alignment of the margin-boxes content. For the moment, it’s not taken into account in pagedjs.

HTML: margin-boxes-vertical-align.html

Result: margin-boxes-vertical-align-wrong.pdf

The result we should get: margin-boxes-vertical-align-correct.pdf

This issue can be resolved by modifying the align-items (flex-start | center | flex-end) property of the flexible boxes created by pagedjs (sample: .pagedjs_margin-top-left for @top-left)

HTML working: margin-boxes-vertical-align-working.html