Actually, I realized I made a mistake when flashing the boot.img file back onto the device. Now that I've got it flashed correctly, I am no longer prompted with the USB Debugging dialog in the beginning.
Make sure you have the following flags set in your default.prop:
ro.debuggable=1
persist.sys.usb.config=mtp,adb
ro.adb.secure=0
and you should be good to go. With these set, it's not necessary to pre-install an APK into the system/app folder to change the ADB_ENABLED settings using Settings.Global.putint(...)