Unfortunatly, this is highly related to Graphviz, and there is not much that we can do.
The only work arround is to specify hidden links between element, to change the layout.
For example:
package foo {
component L1001
note bottom : note1
component L1002
note bottom : note2
component L1003
note bottom : note3
component L1004
note bottom : note4
L1001 -[hidden] L1002
L1001 -[hidden]-- L1003
L1003 -[hidden] L1004
}
But this is not very handy...