My dear, CCS(Leave) Rules will apply to you only when you resign state Govt job (even if on lien) and join central Govt and not in advance.
You may read rule 13 of CCS (Leave) Rules quoted by you:-
(1) A Government servant (other than a Government servant who has been permitted a limited amount of private practice or who has been permitted to undertake casual literary work or service as an examiner or similar employment) while on leave, including leave preparatory to retirement shall not take any service or employment elsewhere, including the setting up of a private professional practice as accountant, consultant or legal or medical practitioner, without obtaining the previous sanction of -
(a) the President, if the proposed services or employment lies elsewhere than in India; or
(2) (a) No Government servant while on leave, other than leave preparatory to retirement shall ordinarily be permitted to take up any other service or employment.
(b) If grant of such permission is considered desirable in any exceptional case, the Government servant may have his services transferred temporarily from his parent office to the office in which he is permitted to take up service or employment or may be required to resign his appointment before taking up any other service or employment.
If a Govt servant (including shortly retiring) tries the to join other deptt in the manner you want then these rules will stop him.
Further, if the university has permitted you to join another post while on leave (most likely without consulting the Central Govt offering you the post) then it cannot be construed as a binding on the Central Govt to accept you in service while you hold a post. Even if someone erroneously allow you to join the audit authorities are not bound to clear your salary bill till such you relinquish previous post.
In case you were permanent (having completed probation) in previous office then you can hold the lien on technical resignation and join service of Central Govt and hold a lien in earlier deptt on earlier post till you were confirmed on new post.
If you still feel that you are wrongly denied permission to join you may file case in CAT.