When I was an Army Recruiter, I ALWAYS explained the DD FORM 1966/4 in detail to the parents before they signed it. This prevented misunderstandings before hand.
Granted, I would tell them that their son/daughter could not even begin the process without it (to include testing or physical examination).
Had you read the form, it would have clearly spelled out that you were consenting to your son's enlistment in the Marine Corps, and that you consented to any and all mental, physical and psychological examinations, that you consent to him being transported to and from a Military Entrance Processing Station via public conveyance, and authorized him to stay in the hotel during the processing. You also signed that you understood that his enlistment could place him in positions of extreme danger, combat, etc., and that no special considerations were given to you as an enticement to sign the form. You released any and all claims against his pay and entitlements as well.
This from said nothing about being a "Consent to Take a Physical." The fact that the DD FORM 1966 is titled "Record of Military Processing, Armed Forces of the United States" and that on DD FORM 1966/4, the part you signed was titled "Section VII - Parental/Guardian Consent for Enlistment" should have been your fisrt clue.
The 90 days start when he signed his contract, not his departure date.
I never heard of a "withdrawn consent" discharge from Active Duty... Only from the DEP. Yes, he can be discharged from the DEP if you withdraw your consent, but once he got on the bus, that option disappeared.
If you want to see what you signed, Google DD FORM 1966/4... You can look at the form, review it in detail, and see that you signed him into the custody of the US Government.
BTW: How can you "forget" about his LD when you had to fill out the enlistment packet for him because of it? Doesn't add up...