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your bottle cage will fall off
I'm only removing one, so that is quite unlikely and even if it was, I don't really use bottle cages on this bike. Full framebag bro.
the screw will hit the battery
The battery might end up below the top rivnut so that's non-issue. If it doesn't then I can use shorter bolt. Actually, that might even be a useful way of holding the battery in place without padding - I could shorten the rivnut then use a nylon screw to hold down the battery and stop it moving around.
One of two things will happen if you succeed in making the back of the rivnut disappear; either your bottle cage will fall off, or you'll never get the bottle cage on in the first place because the screw will hit the battery and the whole bike will go up in flames.