I don't like the explosion score for 1 main reason, it doesn't adjust for weight. You could make the argument that how heavily Bench Press reps is weighted is a control for weight, as heavier players tend to bench more, but I think just looking at those numbers from a large sample of players demonstrates how much variability there is to it.
For edge rushers, I think you are on to something important by looking at agility numbers. Frankly, I think it's influence relative to the explosion score should be even higher. Most players will have a combined short shuttle/3C within a very small range. Compared to the range of the explosion score the relative impact is minimized by simply subtracting one number from another.
I don't know if you are familiar with the work of Justis Mosqueda who developed the "force players" formula. Essentially it's an algorithm based off of explosive tests like VJ and BJ, agility tests (mostly 3C), but then adjusted for player density (weight/height). It does a pretty remarkable job of predicting player performance.