"This being said, it's not overly comfortable. I might try moving the "container" more mid-way up in my pack."
I put my sleeping kit and camp clothes in the bottom of my pack, then the canister, and "options for the day" on top, with odds and ends stuffed along the sides.
It moves the weight of the canister and food up which will help with the way it feels, and will allow the bottom of your pack wrap better around your hips.
If you can, pad the top rim of the canister with a fleece, or similar, so that when you lean the pack against a rock, the aluminum rim of the canister isn't hammering the pack fabric.