This is one of a number of sections which make provision for public authorities which have remits which fall partly within the legislative competence of the Scottish Parliament. This includes bodies dealing only with devolved subjects, but which operate both in Scotland and England, and Scotland-only bodies which operate in both reserved and devolved areas.  Specific provision is made for these authorities because of the effect of section 53.  That section transfers Ministerial function which are exercisable within devolved competence to the Scottish Ministers and removes them to that extent from UK Government Ministers.  In the case of functions exercisable in relation to public authorities - such as functions of appointment, funding or direction - the result could have been an unworkable distribution of functions between the two administrations.
The present section enables such authorities to be designated by Order in Council as cross-border public authorities.  This then disapplies sections 53 and 118-121 from functions which are specifically exercisable in relation to such authorities. (Sections 118-121 translate subordinate legislation procedure and requirements for funding, auditing and reporting to the equivalents for the Scottish Parliament).  Thus all Ministerial functions specifically exercisable in relation to such bodies are left with a Minister of the Crown.
However, the section also requires the Minister to consult the Scottish Ministers before exercising specific functions of appointment or removal or functions whose exercise might affect Scotland other than wholly in relation to reserved matters.  It also imposes a requirement for any report relating to a cross-border public authority, which is required by a pre-commencement enactment (as defined in section 53) or a prerogative instrument to be laid at Westminster, to be laid also in the Scottish Parliament.
The consultation and reporting requirements under section 88 can be regarded as the “default” position for cross-border public authorities.  That position can be modified under section 89 to provide, for example, that certain appointment or direction-making powers should be exercisable by the Scottish Ministers. This allows arrangements for accountability and control to be tailor-made for particular authorities.
Other related provisions are:
Commentary Part V: Miscellaneous and General General