I ended up with same solution by using a select tool after the macro to provide an interim fix.
The issue in my instance related to using dynamic columns in the macro, particular the Select and Dynamic Select tools ("select tools"). When Alteryx tries to determine the columns being passed through the macro before the workflow is run, the select tools will error if no columns are passed. Select tools after Cross-tab tools where only dynamic fields are being converted are an example of this issue .
The workaround is to use the Union tool to guarantee particular columns will be present before using the select tools. This appears to properly fix the macro and using the Select tool after the macro is no longer required.
As for a proper fix, Alteryx needs to provide more control to authors on how dynamic data is determined when processing macros.