Subsection (1) permits subordinate legislation made under certain provisions of the Act to modify the Scotland Act (except Schedules 4 and 5) and subordinate legislation made under the Act.  The relevant provisions are:
Section 30(2) and (4) permit Orders in Council under section 30 to make modifications of Schedules 4 and 5 of the Act, and of other provisions in or under the Act.
Subsection (2)   provides that the reference in subsection (1) to a power to make subordinate legislation modifying the Scotland Act and subordinate legislation under that Act includes that power as extended by section 113.  For example, section 113(4) extends powers so that they include power to make supplementary, consequential provision or transitional provisions, and it may be that modifications to the Scotland Act are necessitated by such supplementary etc. provisions rather than by the main power itself.
Subsection (3) permits subordinate legislation made under certain provisions of the Act to have retrospective effect.  The relevant provisions are:
Powers to Make Subordinate Legislation Details of provisions