For me if the plugin doesn't change folder names in the Project overlay it feels like there's a disconnect between UE4 and SkookumScript. Right now if you rename a blueprint with SkookumScript components you'll have to fix that outside of both UE4 and SkookumScript by renaming folders. Or by being careful not to rename anything at all which seems like a bad workaround.
I'm new to SkookumScript but for me it would make sense if the Show in IDE button always took me to the code I wrote (in my example doing the spinning cube tutorial, renaming the BP and clicking the Show in IDE button takes me somewhere else). Making this the default would make things more predictable in my opinion because if you renamed your BP you would probably want to rename your scripts to that name at the same time. Otherwise you've got a renamed BP with scripts that are not renamed which makes things pretty confusing for me at least.
If that's not how everyone works with SkookumScript I would love for any way of making this possible, dialog box, project setting or anything else.