The issue is that the CF bottles have a slightly larger diameter than the old metal bottles. You may have an older stock on a rifle that's been upgraded to a CF bottle. Also, the CF bottles are not all the same diameter. They vary slightly bottle to bottle and even down the length of a single bottle.
I performed the exact same procedure as you did in order to relieve the pressure on the bottle and stock... A dremel with a sanding drum, a steady hand, and patience. It's a VERY risky procedure but it will give you the best result, if done right. One area to watch is where the curve on the stock interacts with the curve on the front of the bottle. This can be a tricky area to remove material while maintaining the original lines of the stock.
Another way to solve this issue is to install some type of spacer on the bottom rear of the action and a washer at the stock screw location. However, you run the possible risk of ending up with a wobbly stock with this method.
As to your question, Yes, it is a concern as it puts unnecessary strain on the bottle, rifle, and mating threads.
Tom in Colorado