Most of the Atto plugin popups don't use anything but plain HTML <button> classes and so see look a bit 1990s by comparison to buttons used elsewhere in Moodle.

btn-primary for the save buttons at the bottom and btn-secondary for other uses would be nice.

There's a couple of grids (for equations and special characters) that might need to use some custom btn-group CSS to look nice (see https://stackoverflow.com/questions/38261294/how-i-can-make-nice-looking-matrix-of-buttons-with-bootstrap-3 for inspiration)