The jlink tool will require updates to work with modular JARs that are multi-release JARs.

Consider the following with jdk9/dev today:

$ jar tf m1.jar
META-INF/
META-INF/MANIFEST.MF
module-info.class
META-INF/versions/
META-INF/versions/9/
META-INF/versions/9/module-info.class
META-INF/versions/9/p/
META-INF/versions/9/p/Main.class
META-INF/versions/9/p/Type.class
p/
p/Main.class

$ jlink --output myimage --addmods m1 --modulepath m1.jar:$JAVA_HOME/jmods
Error: module-info.class not found for META-INF module

The main issue is that jlink attempts to create the runtime image with all resources in the modular JAR, it should only read the module classes/resources that are appropriate for the target JDK version.

Another part is that jlink doesn't know the target major version and doesn't have any ability to configure the ModuleFinder so that the module declaration for that release is used.