I finally solved the problem and it got nothing to do with websphere.
My project is using maven m2e plugin and in preference "Java EE > Maven > Maven Project Settings" I have click "Set all Maven values".
This change the Dynamic Web Project Output Folder to "src/main/webapp/WEB-INF/classes" instead of "target/classes".
The .classpath file is still referencing "target/classes".
I added this line to my WAR pom.xml:
<build>
<outputDirectory>src/main/webapp/WEB-INF/classes</outputDirectory>
.
.
</build>
And the runtime loading of JSP works as expected!