Unfortunately, we meet Boxing an inline equation shifts the baseline · Issue #4796 · typst/typst · GitHub here. As shown in A snippet to debug font by visualize baseline, cap-height, etc - #4 by Y.D.X, heights in math equations are tricky.
This is because a multi-line math expression, like a fraction, needs to set its baseline at the math axis height (a constant provided by the font, then scaled by the font size), but a boxed frame probably set its baseline with another value or never set it.