This permission check isn't done by the installer, so it means that the mount command indeed didn't get permission from the system to remount /system writable. If you have the chance, you could try if using a different root app (e.g. SuperSU) fixes it. Not sure what I can do about this.
Tired of updating your mod for every new ROM release?
You want give users the possibility to combine different mods without creating tons of different files for all possible combinations?
Then have a look at my Xposed framework
- modifications without APK changes!