Protocol activation of WPF application not working when installed using appinstaller

Question

I have a WPF desktop application that I have packaged into an MSIX package. In the package manifest I have defined a windows.protocol extension to launch the main executable when a specific protocol is used. This protocol activation works fine when I install using the MSIX package directly. The application should be auto-updating, so I created a .appinstaller file that references the MSIX. That also works well, but when the application is installed using the .appinstaller file, the protocol activation does not work. In fact Windows prompt for an application when the custom protocol is used. I have not changed the MSIX package in any way, just referenced it. The MSIX package is signed using a valid bought signing certificate.

The protocol in question provides deep links into the application that users can share using email. For the moment I have to choose to either have protocol activation (install the MSIX directly) or auto-updating (install using the .appinstaller file), but I can't get both to work.

appmanifest.xml

<?xml version="1.0" encoding="utf-8"?>
<Package
  xmlns="http://schemas.microsoft.com/appx/manifest/foundation/windows10"
  xmlns:uap="http://schemas.microsoft.com/appx/manifest/uap/windows10"
  xmlns:uap3="http://schemas.microsoft.com/appx/manifest/uap/windows10/3"
  xmlns:rescap="http://schemas.microsoft.com/appx/manifest/foundation/windows10/restrictedcapabilities"
  IgnorableNamespaces="uap uap3 rescap">
  <Identity
    Name="MyApp"
    Publisher="CN=CompanyName, O=CompanyName, L=City, S=Province, C=BE"
    Version="1.0.0.0"
    ProcessorArchitecture="x64"/>

  <Properties>
    <DisplayName>MyApp</DisplayName>
    <PublisherDisplayName>CompanyName</PublisherDisplayName>
    <Logo>Images\StoreLogo.png</Logo>
  </Properties>

  <Dependencies>
    <TargetDeviceFamily Name="MSIXCore.Desktop" MinVersion="6.1.7601.0" MaxVersionTested="10.0.10240.0" />
    <TargetDeviceFamily Name="Windows.Desktop" MinVersion="10.0.14393.0" MaxVersionTested="10.0.18362.0" />
  </Dependencies>

  <Resources>
    <Resource Language="en-us"/>
  </Resources>

  <Applications>
    <Application Id="App"
      Executable="MyApp\MyApp.exe"
      EntryPoint="Windows.FullTrustApplication">
      <uap:VisualElements
        DisplayName="MyApp"
        Description="MyApp"
        BackgroundColor="transparent"
        Square150x150Logo="Images\Square150x150Logo.png"
        Square44x44Logo="Images\Square44x44Logo.png">
        <uap:DefaultTile Wide310x150Logo="Images\Wide310x150Logo.png" />
        <uap:SplashScreen Image="Images\SplashScreen.png" />
      </uap:VisualElements>
      <Extensions>
        <uap3:Extension Category="windows.protocol">
          <uap3:Protocol Name="myprotocol" Parameters="-s &quot;%1&quot;">
            <uap:DisplayName>MyProtocol Scheme</uap:DisplayName>
          </uap3:Protocol>
        </uap3:Extension>
      </Extensions>
    </Application>
  </Applications>

  <Capabilities>
    <Capability Name="internetClient" />
    <rescap:Capability Name="runFullTrust" />
    <Capability Name="privateNetworkClientServer"/>
    <uap:Capability Name="userAccountInformation"/>
  </Capabilities>
</Package>

myapp.appinstaller

<?xml version="1.0" encoding="utf-8"?>
<AppInstaller Uri="\\someserver\someshare\myapp.appinstaller" Version="1.0.0.0" xmlns="http://schemas.microsoft.com/appx/appinstaller/2018">
  <MainPackage Name="MyApp" Version="1.0.0.0" Publisher="CN=CompanyName, O=CompanyName, L=City, S=Province, C=BE" ProcessorArchitecture="x64" Uri="\\someserver\someshare\myapp.msix" />
  <UpdateSettings>
    <OnLaunch HoursBetweenUpdateChecks="0" ShowPrompt="true" UpdateBlocksActivation="true"/>
    <AutomaticBackgroundTask/>
  </UpdateSettings>
</AppInstaller>