Please don't use the reserved system area at the start of EEPROM for sketch storage. Any EEPROM used by a sketch should start at or past EEPROM_STORAGE_SPACE_START.
It's better to use EEPROM.update() instead of EEPROM.write() to prevent unnecessary writes to EEPROM.
For sound mute handling you should use the library's audio subclass functions. That way, the mute state will be carried over from sketch to sketch.
To test if sound is muted, use audio.enabled(). If it returns true then sound is on, otherwise it's muted.
To set sound on, use audio.on() and use audio.off() to mute the sound. (The Arduboy2 library additionally has audio.toggle() to toggle the mute state.) None of these functions permanently save the state in EEPROM. To save the current mute state to EEPROM use audio.saveOnOff().
If you were to change your sketch to use the Arduboy2 and ArduboyTones libraries, you wouldn't need to do mute testing yourself, as you currently are with the
if(options.mute) statments. Muting would be handled automatically by just using the audio subclass functions.