To activate the handles for resizing an embedded PDF (or video), you have to move the mouse pointer over the PDF from the left only while holding down the left mouse button. No other direction will trigger the appearance of the handles. However, if an embedded PDF (or video) is using the whole width of a column, this no longer works because there is no more space for the mouse pointer to move from left to right. Accordingly, the appearance of the handles is not triggered.
Example video with embedded PDF, image and embedded video:
Note the initial width of the embedded PDF and video. As long as their width is smaller than the width of the column, the handles for resizing can be activated. However, as soon as the embedded PDF or video fills the width of the column, this no longer works.