How does intellij use .classpath files?

IntelliJ IDEA can import Eclipse projects and store dependencies in Eclipse .classpath format, see https://www.jetbrains.com/help/idea/import-project-from-eclipse-page-1.html.

If the container entry in the .classpath file is incorrect. Does intellij provide any way to correct it without backporting to eclipse and reimporting the .classpath file?

No, it either stores everything in .classpath or it imports and stores it in IntelliJ IDEA project format. There is no middle ground here and you can't override/adjust Eclipse .classpath with something stored differently.

Ok.  Thanks!  We should be using a build tool anyway.  That answers my question.  Thank you.