The original lightning was just a piece of code in Bowser's sprite, not its own thing (and definitely not Layer 3). The lightning generator is essentially just cropping out that code and making it into a seperate sprite, so you can use it without adding the entire Bowser too.
It's certainly possible to use ExAnimation on the back area color to immitate the lightning without a sprite, but there's a whole lot of limitations with that (not being able to make it look "random", no sound, etc., unless you use UberASM, in which case you're just recreating the generator sprite anyway).
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