It seems typetools always hides custom axes except Grade, and ignores hidden flags; I checked a 'beta3' font in FontGoggles and https://variable-type-tools.appspot.com and got rather different sets of axes, since in this font, Grade is flagged as hidden (along with Slant) and Round is not...
FontGoggles default:

FontGoggles "show hidden axes" turned on:
TypeTools default:

TypeTools "show hidden axes" turned on:
