I would suggest that much depends on how much of your kit is taken up by your biggest thing: for instance, I rarely shoot much long tele, so it would make a certain amount of sense to have my regular carry stuff be fitted to a bag, and just have a case for the longer glass which I could stick on there. (In actual practice I put my big lens in another bag for my dear one to carry, if it's not on a camera. Usually with a body loaded with slower film as well. And a tripod. But I don't exercise this option without good reason.
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If you have a big lens which you usually don't carry, that's a good occasion to put that lens in a separate case. At least if you already have something comfy to carry the rest in.
If you have a big lens that you expect will mostly be on a camera all the time, this can also be an OK reason to have a case at your belt for it. (The last time I used big lenses or a medium format body or anything like that much, I'd just carry that lens and/or camera and any incidentals in a separate bag, from which I could just remove the big lens+body, sling it, and cache the now-nearly-empty bag somewhere. Which won't work on hikes but is good for sports, events, or whatever. ) Anyway, if you expect the big lens to be on a camera most of the time, it's not the worst thing ever to not get a bigger bag, but just have a usually-empty case at your belt. If you'll be actually chunking the lens around in said bag, you may just want a bigger bag.
Alternately, if you have a kit to which the big lens is central, you carry, you could build the carry arrangement around it, and just get additional cases for any extras you might want on some of those occasions.