Do the U.S. Courts Have the Right to Tell the President Who Can and Can Not Enlist

Three federal courts have ruled against Trump's ban on transgender enlistments. I am neither for nor against this, but I am wondering about the President's power here.

Art. II of the constitution says:

The President shall be Commander in Chief of the Army and Navy of the United States, and of the Militia of the several States, when called into the actual Service of the United States; he may require the Opinion, in writing, of the principal Officer in each of the executive Departments, upon any Subject relating to the Duties of their respective Offices, and he shall have Power to grant Reprieves and Pardons for Offenses against the United States, except in Cases of Impeachment.

Which, in my view, is rather ambiguous, leaving the door open for a plethora of interpretation.

However - and this goes back to elementary school - my understanding of The President is Commander In Chief of the Armed Forces, is that the President's power is absolute. Is it not? Or is that true only if there is a declaration of war? Speaking of which, I understand that the extent to which the President has the authority to use the military without a Congressional declaration of war has been a source of debate. But that notwithstanding... as the President has the authority to determine where troops are stationed, how weapons will be used, etc., does he not have the authority to decide who can and can not enlist?

Do the U.S. Courts Have the Right to Tell the President Who Can and Can Not Enlist