I've noted that there are several weaknesses to the highly touted gradient strokes of Illustrator CS6. My biggest issues are the lack of gradient tool support for stroke gradients (as mentioned in another thread), and the inability to apply a gradient across a stroke, when that stroke ins't centrally aligned.
This, when used in conjuncture with the width tool, would have been a great way to create nice irregular inner shadows or glows.
Hopefully Adobe puts out patches for these shortly. They're both very disappointing omissions.
I don't understand what benefit there may be.
Can you post a sample image containing art as you'd expect to see it and how it differs from what is currently available?
You can always use Effect > Path > Offset Path to move a stroke to the inside or outside of a shape.
On the plus side, I'm finding that I can do what I need and more with the Width Tool. Takes a bit more manual work, but it allows for even more fine-tuning. Double-clicking a stroke width point allows me to set the stroke outside of the shape to zero, which gets the job done.
I'd skipped CS5. That Width Tool mixed with stroke gradients is pretty formidable. Could this resolve the issue you're experiencing with the clipping masks, Mr. Stanowski?