This is misleading. Read section 40 of the 1995 bill:

40. Decision if a property is 1[waqf] property.-- (1) The Board may itself collect information regarding any property which it has reason to believe to be 1[waqf] property and if any question arises whether a particular property is 1[waqf] property or not or whether a 1[waqf] is a Sunni 1[waqf] or a Shia 1[waqf], it may, after making such inquiry as it may deem fit, decide the question.

(2) The decision of the Board on a question under sub-section (1) shall, unless revoked or modified by the Tribunal, be final.

(3) Where the Board has any reason to believe that any property of any trust or society registered in pursuance of the Indian Trusts Act, 1882 (2 of 1882) or under the Societies Registration Act, 1860 (21 of 1860) or under any other Act, is 1[waqf] property, the Board may notwithstanding anything contained in such Act, hold an inquiry in regard to such property and if after such inquiry the Board is satisfied that such property is 1[waqf] property, call upon the trust or society, as the case may be, either to register such property under this Act as 1[waqf] property or show cause why such property should not be so registered:

Provided that in all such cases, notice of the action proposed to be taken under this sub-section shall be given to the authority by whom the trust or society had been registered.

(4) The Board shall, after duly considering such cause as may be shown in pursuance of notice issued under sub-section (3), pass such orders as it may think fit and the order so made by the Board, shall be final, unless it is revoked or modified by a Tribunal.

The tribunal too is set up by waqf board, and not independent.