Yes, you can mail in his 1040X
No, your paper return will not be rejected but it will be delayed. You can include a statement with your return referring to your son's 1040X and what happened. You could even include a copy of his 1040X. You should still mail his original 1040X to the address listed on the instructions when he prints out the 1040X.
You are correct, you cannot uncheck the box, so an explanation is necessary at the bottom of the form.
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