I agree and disagree with you here, though I think I'll have a harder time explaining why I disagree.
I agree because I don't like in-jokes for the sake of in-jokes. When that happens, the joke really does detract from what's going on in the story. So, in that regard, I do agree.
I disagree because I really, really like FLCL, with as much passion as some people feel for baseball. So, I can see the girl on the mountain with a bat, but for all I feel toward baseball, she might as well be holding a tennis racket, a two-by-four, or a broom.
Where as, with a guitar, the joke has another level of context for me, I can see how the bat would give the joke a different context, possibly more universal given that bats are more universally known as "objects for hitting spheroid objects."