I was having the same water in the bilge area issue as well. After a day out, I would have anywhere from approx. 2-5 gallons drain out after pulling the drain plug ( I had previously had a 2013 Yamaha SX192, with the older clean out ports ). Dealer was unable to figure out the source. As mentioned by others in different forum threads, my clean out plug tubes are always full of water too. So, while the boat was on a work rack (or trailer would work too), I removed the drain plug, and used a hose to run water around/over the panel with the screws, and plastic pop up hatch cover. Sure enough, water immediately started coming out the drain plug, confirming water entry. I could not believe how much water was leaking through those areas.
I have had people watch the transom area as I slow down/stop, and unless you really abruptly stop, there is no water reaching the second tier level of the hatch and panel. The water source has to mostly be the water that fills/overfills the new style clean out ports. I do think this newer clean out plug design is a more robust design (the older design failed sometimes, and could blow out), it does appear to be letting more water bypass the seal and get up to and on the panel. So, looks we are obviously going to have to deal with the water intrusion with previously mentioned adding silicone sealers, caulk, new rubber, etc.
Therefore, I agree with what has been said, the design of the panel and hatch could have been better. In my opinion, the panel area would have benefitted from a gasket, and a metal flange type set up, for the numerous screws to attach to. It would of been much more ridged, helping eliminate the flex of the fiberglass and plastics. I unscrewed the panel, and there was literally about 50% sealant coverage the factory had done (no wonder the leaking), and 2 of the screws had already stripped the approx. 1/8" fiberglass they are directly screwed into. That set-up is obviously very weak. I cleaned off all the old silicone, and reapplied with 100% coverage (silicone around plug tubes, and re-clamped) . As I think about it now, might be a good idea to put a bead of caulk or silicone around the little plastic access panel too. Something easy to remove, and redo when needed. That little flimsy plastic access panel just snaps into place, no screws or latches, and I bet it leaks easily too.