Directory tree is rooted on ProgramFiles64Folder so all child folders are also 64-bit. Package@Platform is set to x64 also. For the more ordinary components, this is enforced by an error if Win64=yes is not set on the component. However, this is NOT enforced on a component that installs only IIS 7 virtual directories, apppool, and application. Without Win64=yes set on this component, it installs normally, but the bitness of the apppool is set to enable 32-Bit apps which is not what is expected (64-bit apps don't like running in WOW very much).
At least a warning should issue with Platform=x64 if Win64 is not set on the Component element installing the IIS 7 bits. As a workaround, manully setting Win64=yes on the component works.
Changes to the documentation, especially for creating the AppPool, should inform the developer that the bitness of the apppool is expressly dependent on the Win64 setting of the Component.
Alternately, the WebAppPool authoring should allow express setting of the bitness since this is allowed by IIS 7 and is the appropriate/logical place for setting it.