I agree that it is hard to wrap my brain around the specifics of your problem without a visual, but this is a common issue with hydraulic brakes cables that are not as amenable to kinking or pinching. You might want to take a gander at this thread:
http://www.bikepacking.net/forum/index.php?topic=8271.0It discusses making your own handlebar "standoffs" out of PVC piping or similar materials. The objective is to move the mounted bag a little away from the handlebar. This creates a little gap between the roll (or drybag if using no roll) and the bar. If the distance is set right, the cables can run in that gap without much pinching or damage. Check the thread out to see what I mean. There are a couple of good pics in there that illustrate it well (and there are two pages, so make sure to look at both). And you may already have materials laying around you can use for this.
Hope that is helpful. Personally, I now use a Jones Loop H-Bar which eliminated this issue for me. Prior to that I used mechanical brakes so the pinching was less of an issue. The problem I had in that case was that activating the brake lever rubbed it against the bag and could potentially wear a hole in a drybag or stuff sack.