I'm curious how you set the accelerator key choice, to Super? Does that let you use function keys inside the Ghostty terminal too?
# Use 17 for Ctrl, 18 for Alt, 91 or 224 for Meta, 0 for none.
- name: ui.key.accelKey
type: uint32_t
#ifdef XP_MACOSX
value: 224
#else
value: 17
#endif
// user.js
user_pref("ui.key.accelKey", 91);