I keep mine in one of the end compartments of a 720-230 3-compartment insert. It's a snug fit with the hood reversed, and manufacturing variations seem to affect how well it fits. The tripod ring would want to hang over the edge of the insert. If you want it to be mounted on a body, you'd want one of the taller bags, like the F-7 or the F-802.
In the F-1 or F-2 I lay the camera and lens combo on its side (resting on a few battery boxes) in the main compartment with the 720-230 (F-1x) or the 720-220 (F-2) on the back of the bag for other lenses.
Without the hood, the 720-200 will hold a 70-200 2.8 or 100-400 OK. I don't use the 4-compartment inserts, even though that's what comes with the bags; they just don't let me arrange my gear the way I like.
If I only have one camera, it will fit in the F-3x with a 70-200 mounted and another lens in the main compartment; the top bulges up some, but not annoyingly so.
So I'd really suggest not choosing based on just that one lens, but on all of what you'll be carrying.