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You didn't say whether it was a plastic window or a glass window top.
The only negative I can see to storing it with the top down is the possibility of a plastic rear window taking a "set" from the low temperature. I'm assuming your garage isn't heated, too.
I'm also assuming that the storage period wouldn't be extensive in any case, maybe a few days or a couple of weeks at the outside.
If it were an extended period, several weeks or months, I believe you would be better off to store it with the top up.
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