I'm using the latest version of the ESTK (v22.214.171.124) on Mac OSX 10.7.5 and Mac OSX 10.10.3 and cannot confirm any problems customizing fonts and colors.
On the other hand, I did not try customizing every single option available.
What is your version and OS?
I am on the latest OSX (10.10.4) and using the latest available ESTK (126.96.36.199 Extendscript 4.5.5 ScriptUI 6.2.2)
InDesign is the current version, but thats not relevent here I dont think.
Oh, and on a MacBook Pro Late 2013
Its not a huge biggie, as I run multiple monitors, so I just set that monitor to a much lower resolution!
yes, this is still an issue 8 years later...
every 6 months or so I try and tackle it, spent most of this morning trying everything short of a fresh OS X install, all to no avail...