For input fields, top and bottom padding has different values which makes text not being vertically aligned.
The current value for padding is:
padding: .4em .3em .2em .6em;
This means that top padding is 0.4 em while bottom padding is 0.2 em. This gets noticeable the bigger the font is. In particular this was identified in the particular case of Flow (as illustrated below) but it seems to apply elsewhere.
Making both top and bottom padding to be 0.3em would center the text while keeping the overall dimensions consistent.