Yay! @mitu you are awesome. Thank you!
It turns out that the GPi uses the "windowed" version of the settings, so I needed to add the following to /opt/retropie/configs/all/retroarch.cfgmenu_widget_scale_auto = "false" menu_widget_scale_factor_windowed = "2.75"
For what it's worth I had actually stumbled on this setting when messing around but I set the non-windowed value (because it's full screen... I assumed that meant it wasn't windowed) and when that didn't fix it I moved on.