Transporting Rifle: bolt in or out?

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.

Detroit... Not sure of your local laws but I Think I'd transport it loaded :o
(Just kidding that's what modern sporting rifles and handguns are for)

I don't like to separate bolts mags etc from my rifles because it just seems to make it easier to have a mix up, misplace or lose things I need.
I know what you're saying about the long bolt handles though and have to pull the bolt from my 10TR to close the hard case. I just spoon it against the recoil pad and the egg crate sandwiches it securely when closed.