Cesar,
I think you might be asking 2 different things. With ESXi you do not install the Host Utilities Kit (HUK) since it will not work with ESXi. Instead you use the VSC which is installed with vCenter to configure the ESXi hosts (HBA settings, time out values ect.)
MBRalign is used to align the guest VM file system. You are correct that MBRalign does not work with ESXi so you have to align the VMs (if they require it!) using a full version of ESX or a 3rd party tool that is compatiable with ESXi (Quest, Paragon ect).
If your templates are aligned though evey VM deployed from the template will be aligned and it is a non issue.
We also have some solutions for ESXi and alignment in the works coming soon!
Keith