I got a good deal when buying the bike, and took the SE version with all the boxes, as I am not a big user of them. The side cases are well waterproof and I like the way they attach. The top box has leaked a couple of drops after being out in heavy rain I complained to my dealer in Glasgow and he offered the "hole in the bottom" to let it water back out again. I also complained direct to Honda, however their opinion is that it is not offered as waterproof ( I live in the west of Scotland, only 2 dry days a year ffs!)
My opinion is that they don't have enough complaints about it. I will complain again at next service of course. I also intend to chat with trading standards about it, as really selling an adventure style bike with non-waterproof luggage is not right. In saying that, I find the top box ideal size for day runs.
I'm sure a few more on here will contribute to this