Yours is the same situation I’ve had on my last three pickups. I’ve used the short “gutter” substitutes and attached them by drilling through the horizontal square braces that run through the inside if the topper. I drilled from the inside out for the first bolt and then loosely placed the gutter on the outside to locate the other holes. Once those four brackets are in place, and that’s a bit of a fussy job, any manufactured rack that has tall enough towers to clear the roof will do. (A Pannon products after market rack is the brand I think I used for my next to the last truck. No need to go with the really expensive rack system brands, IMHO)
On my last truck I used a ladder rack made by the topper manufacturer (Lakeland, if that matters) and just mounted it by the manufacturer’s instructions. I did have to modify it a bit to allow straps to pass…
If your truck is wide enough to carry your two widest boats, or if you’re content to carry only one boat, you might not even need to extend the racks further, in which case you’re done.
In my situation, and I suppose most others, the racks needed to be a bit wider. To increase the rack width I’ve used 2X4s long enough to support my two widest canoes for the cross braces. (Of course you want to add a couple extra inches so the straps aren’t in danger of slipping off the very end. A small screw on the very end might be useful insurance if you want…) These can be held to the manufactured metal cross braces by putting carriage bolts (with epoxy in the holes to make things a bit more secure and rot resistant) from the top of the 2X4s on either side of the manufactured rack’s metal cross supports. Hold it all in place with a stout metal strap across the bottom drilled to clear the carriage bolt’s diameter and held in place with insert lock nuts.
If you want you can route out a groove on the underside of the 2X4s to fit the metal bars which then allows the 2X4 height to be slightly higher in the rear to minimize air getting under the canoes and acting like a mini parachute - I think that may improve fuel economy a bit. Just make sure your adjustments don’t cause the curve of the canoe sheer line to hit the roof of your cab… extended cabs exacerbate that issue.
I’ve painted the wooden components on my last two racks and used contact cement to glue carpet on the top of the 2X4s to make life easier on wooden gunwales. Once done, if you’ve used the “mini gutters” the whole rig can be pulled off using the tower clamps, leaving only the gutter pieces on during the off season if you want. On my last truck with the topper manufactured base racks, it was more or less a permanent set up, which I didn’t mind.
There may be a better way of doing this, and perhaps someone else will speak up about it, but this method has served me well for close to thirty years,