JGoSubGraph was designed to relocate all the nodes of a collapsed subgraph to the middle of the collapsed subgraph. The connection points remain the JGoPorts of the original nodes.
Changing the behavior of JGoSubGraph in the general case isn't going to happen in JGo 5.3, but there are a few things you could do in your application to improve the appearance.
Creating a JGoLayer in the foreground and calling JGoDocument.setLinksLayer will insure that that the arrow of the link is always drawn in front of the collapsed JGoSubGraph icon.
There are some other solutions described in your earlier topic: