Oh, and I wouldn't worry about the performance of the list - I know that the algorithm can easily handle tens of thousands of elements quickly, so adding a few dozen plugins shouldn't be a problem. The only problem would be with the panel, but like I said, just keep it closed if you want QD to respond faster. It can also work asynchronously, but I think if you want a quick response most of the time, it should just be closed.
You all might be interested in "Mouse Gestures" available at JustGestures.com
In the grand scheme of other ways to invoke a command, this has proven particularly useful above and beyond the QDSK and even moreso into my OS environment.
Long story short, it watches for "RightClick+Drag" shapes or strokes and performs things like running VI or simulating keystrokes based upon the detection which is particularly powerful in this realm.
Is there any solution for this over last 7 years? Recently I'm facing with such overlapping of same shortcuts issue.
Check out Quick Run. It lets you assign multiple letter combinations to a VI.