It was
always a Federal matter by definition, because immigration issues are under the authority of INS. The regulations requiring State family courts to decide custody were written with this fact in mind.
An unmarried biological father does not get automatic custody in the US. There must be a family court hearing before it is granted.
Juan Miguel was never out of the control of Castro's security men. You have to accept the word of Castro, Reno, and the Clintons that Juan's wishes were being followed in the decisions being made in his name.
Are you sure those regulations applied in Elian's case? Not all laws / regulatons asserted to apply by attorneys (Coffey, in this case) actually do apply.