I'm just a contributor, but I think that your original change of the bookmark button looked good (since it centered the icon on the button).
In my opinion you only need to make this change for the print icon. Also, why not add this line to the already existing rule:
https://github.com/mozilla/pdf.js/blob/master/web/viewer.css#L806.

Can you please squash the commits, see https://github.com/mozilla/pdf.js/wiki/Squashing-Commits