解决方案是使用makeappx.exe解压缩msix包，使用signtool.exe对application.exe和application.dll进行签名，然后再次将其打包到msix包中，并再次对msix包进行签名。
下面是一个基本的PowerShell脚本。

try {
    $CurrentDirectory = [System.IO.Path]::GetDirectoryName($MyInvocation.MyCommand.Path)
    Set-Location -Path $CurrentDirectory
    
    # Set Environment Variable to your Windows Kit so signtool and makeappx.exe could be found
    $env:PATH += ";C:\Program Files (x86)\Windows Kits\10\bin\10.0.19041.0\x64\"
    
    # script assume it will run from same directory as msix package and there will be only 1 msix.
    $MsixFile = Get-ChildItem $buildFolderPath -Filter "*.msix" | Select-Object -First 1
    # Important: FolderName should match with MSIX file Name
    $MsixFolderName = [System.IO.Path]::GetFileNameWithoutExtension($MsixFile.Name)
    $UnpackFolderPath = Join-Path -Path $CurrentDirectory -ChildPath ("UnpackFolder\$MsixFolderName")
    $DllFilePath = Join-Path -Path $UnpackFolderPath "MyMauiApp.dll"
    $AppFilePath = Join-Path -Path $UnpackFolderPath "MyMauiApp.exe"
    mkdir $UnpackFolderPath
    # Unpack the MSIX to a temp folder created.
    makeappx.exe unpack /d $UnpackFolderPath /p $MsixFile.FullName
    # Backup orginal MSIX
    $BackupMsixPath = $MsixFile.FullName + ".bak"
    Rename-Item -Path $MsixFile.FullName -NewName $BackupMsixPath
    # Sign MyMauiApp.dll
    signtool.exe sign /fd SHA256 /a /t http://timestamp.digicert.com /n "Certificate Common Name" $DllFilePath
    #Sign MyMauiApp.exe
    signtool.exe sign /fd SHA256 /a /t http://timestamp.digicert.com /n "Certificate Common Name" $AppFilePath
    #Pack MSIX package.
    makeappx.exe pack /d $UnpackFolderPath /p $MsixFile.FullName
    #Sign MSIX package.
    signtool.exe sign /fd SHA256 /a /t http://timestamp.digicert.com /n "Certificate Common Name" $MsixFile.FullName
}
catch {
    Write-Error "Failed to sign"
}

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