The default mode for an enterprise server is ASCII, since Windows is an ASCII environment. Programs can be run in EBCDIC as long as they have been compiled using directive CHARSET"EBCDIC". At the beginning of a program execution, that is, the execution of a program invoked by the CALL command, the RUN sub-command (of DSN), or by a job step (PGM=), the JCL engine detects the character set of the program. The character set of the program remains constant throughout its execution.
Steps in a JCL job stream can use different character sets. But if a program initiated by a job step then calls another program, it's up to the programmer to make sure that the character sets used by the programs are compatible (for example for call parameters) or that they handle any incompatibilities themselves.