(WiX) Program files shortcut for per-machine install - wix

Question

Following the example here, I added a shortcut to the ProgramMenuFolder that launches my application. (My code is actually simpler because I don't need the extra folder.)
<DirectoryRef Id='ProgramMenuFolder'>
<Component Id='cmpStartMenuShortcut'
Guid='MY GUID HERE'>
<Shortcut Id='StartMenuShortcut'
Name='$(var.ProductName)'
Icon='MainIcon.ico'
Description='$(var.ProductName)'
Target='[ClientDir]myapp.exe'
WorkingDirectory='ClientDir'/>
<RegistryValue Action='write' Type='integer' Root='HKCU'
Key='Software\Company\Product Name'
Name='installed' Value='1' KeyPath='yes'/>
</Component>
</DirectoryRef>
Since my installation is per machine (ALLUSERS=1, Package/#InstallPrivileges='elevated', and #InstallScope='perMachine') the ProgramMenuFolder is the folder for all users on the machine.
My question has to do with the registry value. My understanding is that it's needed simply to provide a KeyPath for the component that contains the shortcut. The sample uses HKCU, which is a per-user location.
Isn't it a mistake to use a per-user value as a KeyPath for a per-machine component?
If a machine has two admins, and admin #1 installs the product, and admin #2 attempts a repair, then Windows Installer won't see the registry value and think that the shortcut is missing and it will install a duplicate, right?
So I tried changing the RegistryValue/#Root to HKLM, but then WiX complains:
error LGHT0204 : ICE38: Component cmpStartMenuShortcut installs to user profile. It's[sic] KeyPath registry key must fall under HKCU.
error LGHT0204 : ICE43: Component cmpStartMenuShortcut has non-advertised shortcuts. It's[sic] KeyPath registry key should fall under HKCU.
error LGHT0204 : ICE57: Component 'cmpStartMenuShortcut' has both per-user and per-machine data with a per-machine KeyPath.
I don't understand why the key must be under HKCU.

Answer 1

That style of shortcut is for a target that might not be installed now nor at the time it is invoked. It creates the classic .lnk shortcut file. It is useful for shortcuts to targets that your installer is not responsible for but might be useful for users of your product to use (e.g. cmd.exe).
Alternatively, a shortcut for a target you are installing or advertising will be uninstalled when the target is unadvertised (product is uninstalled). For example, WiX installs a shortcut to wix.chm called WiX Documentation. The Shortcut element for an advertised shortcut can be made a child of the File element.
Here is a hand-written example:
<Component Id="ProductComponent">
<File Source="$(var.ConsoleApplication1.TargetPath)" KeyPath="yes">
<Shortcut Id="$(var.ConsoleApplication1.TargetName)Shortcut"
Name="$(var.ConsoleApplication1.TargetName)"
Advertise="yes"
Description="Starts $(var.ConsoleApplication1.TargetName)"
Directory="ProgramMenuFolder" />
</File>
</Component>
To insert the Shortcut element into heat's output, pass it the path to an XSL transform. Snippet:
<xsl:template match="wix:File[contains(#Source,'\myapp.exe')]">
<xsl:copy-of select="." />
<Shortcut Id='StartMenuShortcut'
Advertise="yes"
Name='$(var.ProductName)'
Icon='MainIcon.ico'
Description='$(var.ProductName)'
WorkingDirectory='ClientDir'/>
</xsl:template>

Answer 2

What I would recommend doing is simply making the folder as you said, but not placing the shortcut directly under it. Instead make a shortcut element under the component holding the file. You can use the Directory attribute to specify where you want the shortcut to appear.