Should be a user option. Bullets in the gutter are non-standard, but they also are very useful for drawing attention to certain content — I use them like notes in the margin. Changing this will screw up hundreds of Bear documents for me. I know the Bear philosophy is to not have too many settings, but that’s what an “Advanced” tab is for in Preferences. Give power-users the option.
And if you’re not giving users that option, at least allow users to make the gutters as narrow as possible. There’s a LOT of wasted white space on the sides of Bear windows. If I can’t “write in the margins” with bullets anymore, don’t waste space that space with huge gutters.