This is where I mounted my sidekick bar. Yes it will interfere with a bait well unless you use one other than a Hobie brand bait well. There are many available and even home made from a cooler. You can see the cart is not an issue. The sidekick bar is just in front of the scupper holes. I carry the cart upside down in the scupper holes and pass the bungee through the frame to keep it in the kayak in case of a capsize.
The biggest problem is attachment. You cannot reach this area to install through bolts. I used the well nuts but change from the small ones they give you with the sidekicks (they have a bad record of popping out) to using 1-1/2" long well nuts. I have never had them pop out.