but you cannot apply for UI UNTIL the separation has taken place
Yes, you can any
body can file a claim for unemployment benefits anytime. Federal
You're right, you can, but if you do it in the middle of a leave of absence, EDD is going to do a separation issue determination whether you like it or not, and it could very well be treated as a quit without good cause.
http://www.edd.ca.gov/UIBDG/Misconduct_MC_5.htm#DischargeDuringLeaveofAbsenceorTemporaryLayoff
http://www.edd.ca.gov/UIBDG/Voluntary_Quit_VQ_285.htm
And from here http://www.edd.ca.gov/UIBDG/Voluntary_Quit_VQ_285.htm
"3. Is the current unemployment due to the claimant's being on a leave, failure to request a leave, or failure to return to work after the leave has expired?
c. If the claimant failed to request an extension, was the claimant aware that extensions were available?
d. If the claimant failed to request a leave or extension, would the leave have served a useful purpose, or would it have been a futile gesture?"
This person may not be in this situation, but I think he is.
Then for the denial reasons: http://www.edd.ca.gov/UIBDG/Voluntary_Quit_VQ_285_-_Reason_for_Decision.htm
"A. Failure to Request Leave
You quit your last job with (employer name). You did not request a leave of absence to protect your job. After considering available information, the Department finds that you do not meet the legal requirements for payment of benefits."
and by inference, most likely an extension.
"E. Leave Offered, Refused
You left your last job with (employer name) but refused a leave that would have held your job for you. After considering available information, the Department finds that you do not meet the legal requirements for payment of benefits."
Filing a claim willy nilly is high risk in a situation like this unless the OP gives more facts as to just what is happening to him.