After upgrading to 4.25 and regenerating the project, I went through a diff of all the changes in generated code since the previous version. The majority were whitespace and comment changes which were fine.
But I did notice the following which looks like path breakage in the generated Makefile:
Notice the insertion of the '/' preceding 'Src', which breaks the relative path.
A similar change that makes a relative path into absolute is in mx.scratch: