Thank you very much.
I though there were 2 kinds of subsystems, multiinstace and not. From your comment I guess that means that I was wrong and there is not such thing as a "unique instance" subsystem. Unique instance subsystems are just a "special case" of multi instance subsystems.
What made me most confused about it was the fact that in <webapps>/alfresco/WEB-INF/classess/alfresco/subsystems the file I'm overriding is in /thirdparty/default/, not in /thirdparty/default/default so it looks like the context loading class does not treat "regular" classpath directory and extension classpath directory the same way.
Not a big deal once you know it, but maybe worth a very very very low priority improvement request in the JIRA ? I'll try to make it clearer in the Wiki as soon as I have some time.