^
Water will not be an issue whether the base is left in or removed. Personally, I would keep the base in place for two reasons: First, it acts as a partial barrier to heat rising up the header and exhaust. Secondly, with the base left in place along with the cold air tube, a very tiny amount of cooler air will be directed towards the filter. Not much, but better than nothing.
Ideally, a filter should be enclosed in an airbox to completely isolate it from heat and to provide a vacuum to which cooler air can be pulled in. This is how the factory cold air works, and in a much greater way, how ram air and cowl induction work.
OP. l suggest leaving the base in place.