I say all this without having used Windows Server Backup, so take it for what it's worth. A lot of this is going to depend on how it writes data back to the drive. If you need to restore the OS, follow the directions here. Assuming that your databases are not on the OS drive (please tell me you have separate data and log drives) then sizing shouldn't matter too much here.
I don't see anything regarding formatting cluster sizes in my searches, so assuming best case here's what I'd try. Get the OS up and running, and then use DISKPART (or go to diskmgmt, whatever) to format the data drive the way you want. Then use WSB to write the data to the drive, without formatting it.
The other thing to consider here is the state of the drives you're restoring. If the hardware is fine, but you just had corruption of data, then you can just restore the volume without reformatting anyways. If the hardware went bad, you'll need to prep it before restoring the data.
All that to say that I haven't found a way to change the cluster size during the restore itself.