Can you include expressions in the "Output Files" section of a build rule in Xcode? Eg:
$(DERIVED_FILE_DIR)$(echo "/dynamic/dir")/$(INPUT_FILE_BASE).m
Specifically, when translating Java files with j2objc, the resulting files are saved in subfolders, based on the java packages (eg. $(DERIVED_FILE_DIR)/com/google/Class.[hm]). This is without using --no-package-directories, which I can't use because of duplicate file names in different packages.
The issue is in Output Files, because Xcode doesn't know how to search for the output file at the correct location. The default location is $(DERIVED_FILE_DIR)/$(INPUT_FILE_BASE).m, but I need to perform a string substitution to insert the correct path. However any expression added as $(expression) gets ignored, as it was never there.

I also tried to export a variable from the custom script and use it in Output Files, but that doesn't work either because the Output Files are transformed into SCRIPT_OUTPUT_FILE_X before the custom script is ran.

Unfortunately, Xcode's build support is pretty primitive (compared to say, make, which is third-odd years older :-). One option to try is splitting the Java source, so that the two classes with the same names are in different sub-projects. If you then use different prefixes for each sub-project, the names will be disambiguated.
A more fragile, but maybe simpler approach is to define a separate rule for the one of the two classes, so that it can have a unique prefix assigned. Then add an early build phase to translate it before any other Java classes, so the rules don't overlap.