I have two Ibanez RGs with JBs in the bridge position, but they sound quite a bit different to me.
In the first (RG220B), it's a basswood body with pickups mounted on pickup rings, maple/rosewood neck/fb, and an F spaced JB. In the second (RG350m), it's a basswood body with pickups mounted on pickguard, maple/maple neck, and regular spaced JB from the Hot Rodded Humbucker set. Both guitars have Ibanez floating trems.
In the first guitar, it sound crystal clear, has an amazing tone, and I absolutely love it.
In the second guitar, it sounds kind of muddy and not so clear no matter what I do with my amp.
After listening to the video you made after alterations, I find the same thing as you originally posted. The black one is more clear and articulate, the yellow tends to be slightly warmer but also a bit muddier.