OK I found a solution I like. It still involves modifying the 1F software but at least is not a total hack. I will provide this solution in case others run into the issue where the external adapter is not taking precedence over the internal wifi.
The solution is to entirely disable the internal wifi which is done by editing the file /boot/config.txt. However, the /boot file system is mounted read-only by default so first you have to remount it read-write:
sudo mount -o remount,rw /boot
Now you can edit /boot/config.txt with your favorite editor and add the following:
dtoverlay=pi3-disable-wifi
Now reboot and only the external wifi adapter will be recognized by the OS.