They do exactly the same if you select the no reboot option when creating the AMI directly from EC2. This basically creates a snapshot that can potentially be in a inconsistent state. For example, you are risking more having an inconsistent state if you are doing a lot of disk writes when creating the snapshot.
If you want to create a snapshot in a “consistent” state you would have to shutdown your instance first and then take a snapshot and then restart your instance. This is why the AMI creation option from EC2 is pretty useful because you don’t have to stop and restart. Amazon takes care of it and also the IP address doesn’t change on your instance. (If you stop/restart your instance your IP address actually changes)
I’m not really sure why Amazon doesn’t have a warning if you take a snapshot directly from the volume but from the volume point of view it really doesn’t matter whether the volume is being used by a running or non running instance (it only cares whether it’s attach or detatch to no effect on creating snapshots)