JDK-8258411 altered the make/common/Modules.gmk custom extension location such it is now no longer able to customize the module lists:
https://github.com/openjdk/jdk/commit/a244b822936d983609ea1eb47885efc59c2d0d30

make/conf/module-loader-map.conf initializes the module list variables after the IncludeCustomExtension thus discarding any custom module settings.
The position of make/conf/module-loader-map.conf needs to be before the IncludeCustomExtension.