Odd, I don't have the problem with the storage areas filling with water - I imagine your 2005 200H is very similar to my 2007 200H with Sunsport seating. Sounds like you are talking about the areas under the seat cushions on either side of the cooler, rather than the storage areas under the lift up sundeck to either side of the engine compartment. I am surprised those areas would fill with water as the entire bench is removable, to facilitate working on systems in the engine compartment. You most certainly can cut into the corners of the bench - apart from the cushions and hinges, the bench is almost entirely constructed from starboard.
On the cupholders, I've heard that the SS cupholders do not have drain holes. The white plastic cupholders on my boat do have drain holes, and I know that on mine there is no additional tubing running from those drain holes, I'd think you'd be fine drilling your own drain holes. A call to FW Customer Service on this might not be a bad idea. I personally wouldn't hesitate, but then I have plans to drill holes to add four more cupholders to mine, so consider the source of this advise.
