Here's one solution (works for any .exe in fact), not sure it's officially sanctified though:

Once you have created your packaging project, instead of adding a reference, just change the .wapproj, add these properties (adapt to your context):

  <PropertyGroup>
    ...
    <AppxBundlePlatforms>x64</AppxBundlePlatforms>
    <EntryPointExe>MyApp.exe</EntryPointExe>
    ...
  </PropertyGroup>

  <ItemGroup>
    ...
    <Content Include="..\MyApp\bin\x64\Release\net10.0-windows10.0.22000.0\publish\MyApp.exe">
      <Link>MyApp.exe</Link>
      <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
    </Content>
    ...
  </ItemGroup>