Unfortunately, most fancy cases don't really make allowance for this. But, at least in these two cases, it's still possible!
Standard bass case-
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Screwbell bass case-
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In the standard case, the rod is held in place by some foam inserts and can't contact the horn in any way.
In the screwbell case, it makes just slight contact with my Gb side so I put a rag in to prevent scratching. Otherwise it has no room to move and won't ding anything.
Of course, YMMV with different horns and interior setups.