When you generate XSLT or XSLT2 code and the mapping uses Global Resources, this does not affect the generated XSLT stylesheet in any way. With or without Global Resources, the input and output files are not a permanent assignment and can be specified flexibly anyway when you run the XSLT stylesheet in your XSLT processor. The same applies for generated XQuery code.
An exception to this is the DoTransform.bat file generated for RaptorXML execution. Any Global Resources used by the mapping will be resolved to actual paths in DoTransform.bat, taking into account the value (configuration) which is currently selected from the Global Resource drop-down list.
For information about supplying Global Resources to RaptorXML, refer to the RaptorXML documentation (see https://www.altova.com/documentation.html).