The line item #8 in JDK-8212936 says:
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8.) In src/jdk.packager/unix/scripts/jpackager:

This file resides in a non-standard directory. We have a small list of directories that are supposed to come after the $MODULE/share|$OS/ part of the path, and "scripts" is not one of them. While there is no rule "forbidding" new kinds of directories, I strongly recommend against this.

Looking more closely at the file, I wonder if you really need it? It's sole purpose seems to be to launch java -m jdk.packager/jdk.packager.main.Main. For that, we have a much better solution. Just change make/launcher/Launcher-jdk.packager.gmk to include the following contents:

$(eval $(call SetupBuildLauncher, jpackager, \
    MAIN_CLASS := jdk.packager.main.Main, \
))

It will create a "jpackager" binary. Which works for Windows too, so maybe you won't even need that Windows executable, if that too is just a launcher?
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Basically, we have a jpackager native launcher on windows but use this script on macosx and linux.
We should create native launcher for all platforms.