So it turns out some of the optimization done in the original Windows 7 script does break Modern UI Apps on the linked clones if you use QuickPrep. Trying with an un-optimized image worked with QuickPrep without any issues.
I applied the tuning manually from the Horizon View Administration document by following the Creating and Preparing Virtual Machines section. So far, it seems to work nicely. So my suspect is on IP Helper service, Windows Firewall service, and UAC now. Since you need Windows Firewall service to be set to Automatic for Blast HTML access agent, and UAC is required for Modern UI apps, this shouldn't be much of a compromise.
Hopefully VMware updates their white paper guide to include Windows 8 soon.