I can see your point re - the likelyhood of water being sucked up via that original length inner tube , if the water got up to that level by getting in through the screwed plastic bottom plate . I'd rather attempt to find another place to draw in cold air that's not sited flush with the floor. If that's a non starter space wise then making a better seal when fitting the bottom plate would help keep water out when presented with road water deeper than estimated. NOT actually too difficult BUT at some point each year it's got to come off for a filter change , otherwise I'd use Sikaflex --- nothing would get in , even in flooded roads sealed with that stuff.
Possibly the orange sealant that I use for gearbox/diff instead of gaskets might do it --- my oil's never leaked a drop from the race car using that(need to check the receipt , forgotten what it was now)