(d) Deposit and disposition of revenue. All taxes, and any interest and penalties relating thereto, collected or received with respect to the supplemental petroleum and aviation fuel business tax imposed by this section up to and including March thirty-first, nineteen hundred ninety-three shall be deposited and disposed of pursuant to the provisions of section one hundred seventy-one-a of this chapter. Except as otherwise provided, on and after April first, nineteen hundred ninety-three, all taxes, and any interest and penalties relating thereto, collected or received in any month with respect to such supplemental petroleum and aviation fuel business tax imposed by this section, together with any other moneys specified in this chapter to be deposited under this subdivision, shall be deposited, on or before the fifteenth day of each succeeding month, proportionately into the following dedicated fund accounts without priority; sixty-three percent in the dedicated highway and bridge trust fund established pursuant to section eighty-nine-b of the state finance law, thirty-four percent in the dedicated mass transportation trust fund established pursuant to section eighty-nine-c of the state finance law to be distributed as follows: eighty-five percent of such amount shall be allocated to the New York city transit authority and its subsidiaries and the Staten Island rapid transit operating authority and fifteen percent of such amount shall be allocated to the Long Island Rail Road Company and metro north commuter railroad company in accordance with the procedures for payment and distribution specified in section one thousand two hundred seventy-c of the public authorities law, for payment, subject to appropriation, to the metropolitan transportation authority dedicated tax fund established pursuant to section twelve hundred seventy-c of the public authorities law, and three percent in such dedicated mass transportation trust fund to be distributed, subject to appropriation, for purposes authorized by section eighty-nine-c of the state finance law, to entities other than the mass transit operating agencies which receive money from the metropolitan transportation authority dedicated tax fund. Notwithstanding any general or special law to the contrary, other than a law which makes specific reference to this sentence of this section, so long as such metropolitan transportation authority dedicated tax fund shall exist, any appropriation from the dedicated mass transportation trust fund to the metropolitan transportation authority, its affiliates or its subsidiaries shall be deemed to be an appropriation to the metropolitan transportation authority and the total amount paid pursuant to such appropriation or appropriations or section thirty-one of chapter fifty-six of the laws of nineteen hundred ninety-three including the second clause of the first sentence of subdivisions a and b thereof, shall be deposited to such metropolitan transportation authority dedicated tax fund and distributed in accordance with the provisions of section twelve hundred seventy-c of the public authorities law. Prior to making deposits as provided in this subdivision, the comptroller shall retain such amount as the commissioner may determine to be necessary, subject to the approval of the director of the budget, for reasonable costs of the department in administering and collecting the taxes deposited pursuant to this subdivision and for refunds and reimbursements with respect to such taxes, out of which the comptroller shall pay any refunds or reimbursements of such taxes to which taxpayers shall be entitled. Provided, further, however, that, prior to such deposit, from the amounts so collected or received during the period commencing on January first, nineteen hundred ninety-four and ending on March thirty-first, nineteen hundred ninety-four, an amount equal to the portion of the taxes, interest and penalties so received or collected resulting from the amendments made by sections forty-two, forty-three and forty-four of chapter fifty-seven of the laws of nineteen hundred ninety-three shall be deposited and disposed of pursuant to the provisions of subdivision one of section one hundred seventy-one-a of this chapter.