You really shouldn't have an issue with the tool poking you in the back. I'm not sure if you're concerned with one of the allen wrenches or something poking you or just feeling a metal lump on your back. I'll address both...most multi-tools fold nicely and securely. One of the individual tools will not unfold and poke/jab you in the back. Once it's in your pocket folded up, it won't unfold. Also, I know some of the park multi-tools come with their own nylon carrying case if you are really concerned with that. As for feeling the big metal lump in your back pocket, you'll forget it's there after one minute. The way the back pockets are designed makes it very comfortable to carry items. You'll forget that you have a multi-tool and tube in your pocket.

The other option would be to utilize an extra water bottle cage (if you have one). I was flipping through a catalog the other day and saw they make a container that fits into your cage to carry tools, tube, keys, etc. It had a larger opening than a water bottle, but I would think a standard bottle could work also.