I'd enjoy using '.jar"-Files as type-map files rather than standard ".var"-files using Content Negotiation.

Well, this really is my configuration:

<Directory "${APACHE_PROJ}/htdocs/foo">
  AddType application/x-java-archive .jar
  AddHandler type-map .var

  <Files *.pack.gz>
    AddEncoding pack200-gzip .jar
    RemoveEncoding .gz
  </Files>

</Directory>

...working well and delivering from subfolders not surprisingly with foo.var:

URI: foo

URI: packed/foo.jar.pack.gz
Content-Type: x-java-archive
Content-Encoding: pack200-gzip

URI: unpacked/foo.jar
content-type: x-java-archive

Renaming file foo.var to foo.jar and altering the configuration to AddHandler type-map .jar doesn't work, this provides the foo.jar in the root directory immediately.

Without some type of type-map (presently .var inside your situation) to allow the browser/server settlement evaluate which variants of the .jar files may be used, it is simply likely to grab the very first .jar it finds and serve it. Being as Apache's default handler for any .jar file would be to serve it, you would need to RemoveHandler .jar after adding the kind-map handler to see it as you would like, but this could stop the files from being offered when needed.