If you ask me, the game should allow you to that even with auto-bolting because there is no reason your character shouldn't be able to stop working the bolt and club/stab someone instead.
Manual bolting should be there for three reasons, in my opinion:
a) being able to chose if you want to stay zoomed in and not have your character's hands block your view so you can see where or if you hit your target.
Though, imo, it should also be an option to just hold the aim down sights key down as long as you want to look and let it go as soon as you're ready to bolt (the game can autobolt for you then, if that's what you chose in the options). The "sniper" in Far Cry 2 works that way and it's great.
b) increase immersion because making you actively chose to cycle the bolt makes it feel more like you are cycling the bolt. Personally, I think the immersion would be even greater if bolting was a separate key (default to the same as "fire", but bindable to another key) because then you'd be pressing the designated bolting key, i.e. you chose to bolt. Having to press "fire" again, to me, feels more like being impatient with the weapon and making it bolt, same as you would reload empty weapons by clicking "fire" again in many other weapons.
c) emptying your rifle so you can reload it with a fresh clip without having to fire it and giving away your presence. This requires bolting to be set to a different key though, which isn't possible in RO2 (at the moment).
I really don't think being able to hit people again sooner after you shot your rifle (because you can start clubbing and stabbing right away without having to wait for the autobolting to finish), or an artificial speed-boost over auto-bolters should be the point of manual bolting.
I've been saying this since before manual bolting was introduced in RO1 though and it's still on the same key so I don't expect this to change.