Microsoft.Windows.CsWinRT.targets defines a property CsWinRTAotExportsEnabled:

   <!--
      If the AOT optimizer is enabled, and we're publishing with NativeAOT, automatically set CsWinRTAotExportsEnabled as well.
      Only do this if the property is not already set by the user, so we respect any existing preference.
    -->
    <CsWinRTAotExportsEnabled Condition="'$(CsWinRTAotExportsEnabled)' == '' and '$(CsWinRTAotOptimizerEnabled)' == 'true' and '$(PublishAot)' == 'true'">true</CsWinRTAotExportsEnabled>
    <CsWinRTAotExportsEnabled Condition="'$(CsWinRTAotExportsEnabled)' != 'true'">false</CsWinRTAotExportsEnabled>

However, PublishAot being true does not indicate that a build was actually an NAOT build, instead it indicates that a publish build will produce NAOT’d assemblies. This results in build failures when expected artefacts don’t exist. For example, WinRT.Host.dll is outputted conditional on CsWinRTAotExportsEnabled not being true.

I'm not sure how often this idiom is used across the targets files, so I can't recommend a specific fix, but it's probably something like setting CsWinRTAotExportsEnabled to true in a target that runs only before the publish target and ensuring that the only place PublishAot is checked is when that's set.