The /boot partition is the least important of all IMHO, as it gets pratically no I/O on it, apart from when you do a kernel install and an initrd generation.
In fact you could also unmount /boot in a running system without problems...
Inside the white paper there are some points that are kept superficial.... system disk vs data disk .... if you have an application server you don't get another disk only to accomplish this division between data and system....
They don't take in mind what is system management and administration...
You start from the bottom and you have vmfs that is aligned, virtual disk that is aligned (both automagically if done inside vcenter server)
btw, as far as I know you should not do operations such as mv or cp for virtual disks, considered as files of the vmfs file system: you are not garanteed to have an aligned resulting vmdisk file this way....
And arriving at the top side, I think it makes sense to align all the partitions. Infact I setup a kickstart file (but working with templates this part could be less important actually when you have done once) so that I could align all the partitions, moving the disk partitioning to the %pre section .
