To import an NTDS Store Certificate... not yet tested.

Import-NTDSCertificate.ps1

# Bennett @ https://stackoverflow.com/questions/21895800/powershell-script-to-install-certificate-into-active-directory-store
# Modified/Simplified

Function Import-NTDSCertificate 
{
    [ CmdletBinding () ] Param (

        [ Parameter ( Mandatory ) ] [ String ] $File     ,
        [ Parameter ( Mandatory ) ] [ String ] $Password ,
        #Remove certificate from LocalMachine\Personal certificate store 
        [ Switch ] $Cleanup )

    Begin
    {
        IEX "Using Namespace System.Security.Cryptography.X509Certificates"

        Write-Verbose -Message "Importing PFX file."
        
        $PFX            = [ X509Certificate2 ]::new()

        $PFX            | % { $_.Import( $File , $Password , [ X509KeyStorageFlags ]::Exportable ) }

        $PFX.Thumbprint | % {

            If ( $_ -ne $Null )
            {
                $Paths  = ForEach ( $I in "" , "\Cryptography\Services\NTDS" )
                {
                    "HKLM:\Software\Microsoft$I\SystemCertificates\MY\Certificates\$_"
                }
            }
        }
    }
    
    Process
    {
        Write-Verbose -Message "Importing certificate into LocalMachine\Personal"
        
        $Store          = [ X509Store ]::new( "My" , "LocalMachine" )

        $Store          | % {

            $_.Open( 'MaxAllowed' )
            $_.Add( $PFX )
            $_.Close()
        }

        Write-Verbose -Message "Copying certificate from LocalMachine\Personal to NTDS\Personal"

        $Splat          = @{

            Path        = $Paths[0]
            Destination = $Paths[1]
            Recurse     = $True
        }

        CP @Splat
    }

    End
    {
        If ( $Cleanup )
        {
            Write-Verbose -Message "Removing certificate from LocalMachine\Personal"
            
            $Splat      = @{
                
                Path    = $Paths[0]
                Recurse = $True
            }
                
            RI @Splat
        }
    }
}