I have a custom Sunbrella cover, and still a substantial amount of water finds its way, at times, into the bilge. It's getting in there while the boat is on the trailer, because if I pull the drain plug immediately after I pull up the launch ramp, very little water comes out.
I think(??) I know how it gets in there. Some comes from around the anchor locker, as well as the cupholders in the bow. I think the majority of water gets in from around the rear jump seats. Even though the cover runs to the gunwale (and has snaps), if I remove the jump seats, there is almost always water there after a rain storm. The only thing I can think of is that, with the bow high on the trailer, rain water is running down the gunwales (under or inside the cover area) and then into the boat when it reaches the stern.
I need to get under the cover, and have someone else run the hose on the front of the boat, to confirm that's what is happening. But both of my 225s have done this.