[Nick Payne]

No, the size of the equations does not change when the font size is changed.

Yes, setting justification to off gets the equations centred on the reader screen (it is a kepub).

I had a fiddle with the style used for the images to see what improvement I could get for their display on the reader. It doesn't work too well, as even just the single line equations vary considerably in their native height and width, and setting a specific value in the style for the width or height (as opposed to auto) gives quite a different scale depending on what is in the image. For example, both the attached images are single line equations, but have different heights and scale quite differently unless height and width are left at auto.

I'll have to try your other suggestion, of using Imagemagick to enlarge all the images by the same amount.

Edit: I used Sigil and Imagemagick to enlarge all the png images to 150%. That makes them much easier to read on the Aura HD.