I don't think there is an issue with the waterproofing, it is well made and all of the seams are sealed. If you use the handi duffels inside, I would say that there is no way it would leak.
I decided against the roof rack as I wasn't happy about the way the rack fitted.
In a heavy downpour it's possible (or likely) that the retaining strap would get wet and allow water into the car.
The Handirack is just superb.
I have had one for years, stowing in a small satchel. The pump I have found is very effective, and never needed two people to pump or deflate.
We have carried our Canadian Canoe many times on this without any problems, Its a simple cheap and VERY effective alternative to bars or racks or other paraphanalia.
It is well made, doesn't scratch and with a plethora of secure D rings for tying down. Thoroughly recommended.
I have an older version of one of these racks, and wouldn't be without it. Packs away into a very small bag, and the rack in use is very effective and versatile, useable on a huge variety of vehicles, couple of minutes to fit and happily carrying, amongst much else, a 35kg Canadian canoe.
There is a lot of prejudice against these, as not being "proper" in some sense.............so wrong.
Superbly capable and versatile roof rack.
I have had one for years and carried Canoes, Kayaks, Surf Boards, bits of tree and heaven knows what else.
Excellent quality and thoroughly recommended :-)