Looks like the new component patch (LD96SP1-CP_2015-0114) sorta addresses the issue. It fixes the %Corename% issue but the core certificate is still problematic if you are using Auto Sync. You can work around this by not using Auto Sync and instead using the Copy to Other Core(s)... function. When you copy to another core from the context menu, it leaves the item 'unlocked' instead of making it 'read-only' which happens with Auto Sync.
In working with this, I realized that my workaround listed above was more work than it needed to be because you could just disable Auto Sync and use the copy function and just edit it on the other end.
...which means that the only thing this patch actually helps with is saving us the job of editing the core address field. Oh well.
PS - you have to install the patch on both your sync core and you target core for this to work. If you only put it on your sync core, you get either explicit %fqdn% or %corename% variables in the core address field.