Hmmm.. Think of some of the effects currently in Eclipse.
Eclipse highlights variable names when you click on them. Since there could be same-named variables in other classes it might make sense at first to do the highlighting in all visible code panes, but at the same time, those same-named variables aren't necessarily the same type and may not mean the same thing. So Eclipse only highlights in the current pane.
When you run a search in files, it does makes sense to highlight the variable names (or whatever search string you used) in all panes at the same time, because now they all should have the same meaning to you.
Does the plugin you're adding makes sense to happen in all visible panes?
I always have more than one code pane open. I develop Python at work and usually have Eclipse dragged across two wide-screen monitors. On occasion I actually have three code panes open. This helps when looking at three levels of the stack I can switch between them using the call stack and not lose my place in a different frame. Admittedly it ends up looking like a cockpit after a while, but I can switch between different workspace layouts (Code, Debug, Install, NSIS scripts, etc) when it gets too cluttered.
(BTW what is your plugin going to do?)