How to align the top of an admin pointer to the target element?

that’s a great question, Alex!

Not exactly an answer to the question, but the following will work:

jQuery('#menu-settings').first().pointer( 
    {
        "content":
            "<h3>Pointer header<\/h3>" +
            "<h4>Pointer subheader<\/h4>" +
            "<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Levatio igitur vitiorum magna fit in iis, qui habent ad virtutem progressionis aliquantum. Rationis enim perfectio est virtus; Sed ego in hoc resisto; Quid, de quo nulla dissensio est? Duo Reges: constructio interrete. Bestiarum vero nullum iudicium puto. Si enim ad populum me vocas, eum. Mihi, inquam, qui te id ipsum rogavi? Falli igitur possumus. Quas enim kakaw Graeci appellant, vitia malo quam malitias nominare.<\/p>",
            
        "position":
            {"edge":"top","align":"left"},

        "pointerClass":
            "wp-pointer arrow-top",

        "pointerWidth":420
    }
).pointer('open');

This will create a pointer with an arrow on the top edge of the box, rather than the left edge. The box hangs below the target element.