Regarding pulling this off with AE, I still think it's possible. It requires some "trickery" perhaps and maybe even some clever math when using the CC cylinder. Or maybe I'm not clear on exactly what you're trying to achieve.
So to be a little more precise: as an example, let's say you have 3 panels of 720x480 video, each side-by-side, in a comp. That comp would be 2160 pixels wide. (720 x 3) You'd put this into another comp with size 720x480 and apply the CC Cylinder to this embedded comp. There's a problem. You mentioned it, I alluded to it. The left edge of video pane 1 is going to butt straight up against the right edge of video pane 3, once it's inside the cylinder. As you said, "it wraps the image completely into a cylinder". So the fix is to have a much wider comp than just 2160 pixels. It's a numbers game. You have to have enough horizontal width in the comp receiving the CC Cylinder to start eliminating the distortion.
Here's a simple movie showing my interpretation of your project. There are 2 comps: the yellow "video pane" and the blue "video panes". These are embedded into another comp. But both are very wide comps with the CC Cylinder applied to them.
Here's a screenshot of what the blue panes really looks like. How does this example differ from what you're trying to achieve?