There is a drain(s) that I'm sure you noticed for both the main engine hatch (when you use the hydraulics) and for the 'day' hatch.
Both drain out thru the top of the engine area to the stern.
Water - regardless of canvas can get in everywhere - especially down the gunwales and into the back part of the boat and if an older model 3560 (ie: pre 2005), just at the base of the rear of the side windshields.
Regal since fixed that with improved drainage pathways.
Therefore, water could get into the engine hatch 'drainways' regardless if you have the canvas on all the time or obviously when you take the carpets out to do a deep inside cleaning.
However, having said that, I was down in the engine room one day and noticed a drip of water on my head (from around the light area). I noticed that there was a crack (not all the way thru, more like a de-lamination) in the fiberglass on the roof of the engine room hatch cover. It somehow was collecting water.
The dealer has since fixed that and no problems since.
PS: I should also add maybe to look at the other obvious thing. There are various drain holes in the drain runways for both the main and day hatch. If you have pets (I have two dogs) or even if you don't, those drain holes can get filled with gunk or hair and minimize the effectiveness of the drain run ways which might cause an overflow onto the geni.