Subsection (1) provides that any statutory provision, or any provision not contained in an enactment, requiring a Ministerial function to be exercised only with the agreement of, or after consultation with, another Minister of the Crown should cease to have effect when the function is exercised by a member of the Scottish Executive by virtue of section 53. Section 126(1) defines “Minister of the Crown” as including the Treasury. “Agreement” is intended to include also requirements of consent, concurrence or approval.
Subsection (2) defines “statutory provision” for the purposes of subsection (1) as any provision of any pre-commencement enactment (as defined by section 53(3)) other than paragraph 5 or paragraph 15 of Schedule 32 to the Local Government, Planning and Land Act 1980.  Paragraph 5 of Schedule 32 to the 1980 Act confers a power upon the Secretary of State, with the consent of the Treasury, to make an order designating an enterprise zone.  Paragraph 15 confers a power to modify such an order, again with the consent of the Treasury.  This ensures that the consent requirement is not removed by subsection (1).
Paragraph 1(2)(d) of Schedule 4 lists the provisions requiring the consent of the Treasury amongst the enactments protected from modification by the Scottish Parliament.  By virtue of Part III of Schedule 4, the function of giving consent in each case will not transfer to the Scottish Ministers.
Commentary Part II: the Scottish Administration Details of Provisions