right now these values are hardcoded within the app. for example, the test for the afdko seems to be whether or not the binaries show up in the adobe-recommended ~/bin/FDK/Tools/osx
ttfautohint is a bit more mysterious (i can’t figure out how to get it to enable the ttf autohint checkbox to work even though mojo.compile.hasTTFAutoHint returns true for my version of ttfautohint installed via homebrew).
regardless, it would be easier to debug this behavior if these search paths were easy to set. i think the current behavior probably satisfies many common-cases, but i suspect that there is wide variability in the location of sundry binaries.
thanks!