When you folks are transporting your rifles, especially for long car rides, do you normally keep the bolts in place or store them separately?

I noticed that, when carryign two bolt guns in my range bag (Midway drag bag) the oversize knob on the rifle on the left would jut into the padded divider and make it difficult for the rifle on the right to fit in the case and still allow the zipper to zip. I recently put on another bolt handle that puts the knob even farther out to the side, and, while I could put that rifle on the right, I'm worried that such a prominent point could make toting that gun dangerous. Dangerous to the gun, I mean.

Along with the drag bag, I also have an SKB iSeries hard case. The foam is a weird setup with egg crate foam glued to a big block of polystyrene. This is going to make trimming something of an odd pursuit. When I toted one rifle to Virginia in it, I had to remove the bolt to get it to close. I notice a heck of a lot of pictures of hard cases have separate cutouts for the bolt, so when I do figure out how to deal with the styrofoam block that may be something I could do.