If the truck came in with the 2 non working original keys that didn't work before you cleared them , then there is probably a circuit problem in the immobilizer system that needs to be diagnosed and repaired .

You need an IDS. The IM is hit and miss with Ford's in my experience.

No, the BCM can only be programmed with an IDS. You can try a programmable
module installation with your Autel. It downloads the data out of your old module and
loads it in to the new module. The Jbox with only program engine and transmissions
on Fords.
I have installed ABS modules using the programmable module function with no
trouble, it has not worked for me on PCM's that I have tried however.
You could try an uninstall the Ford program from you tablet and reinstall if you have a
current subscription. Maybe your Ford program got corrupted during an update. I had
trouble with a 2014 F150 when trying to program keys, I got a security access not
granted error, I had trouble with a Lincoln too, it would only program 1 key, the second
key would not take. It seems Ford's are hit and miss with the Autel.