Get owner of ~5 million files and folders using Powershell and Robocopy
Your robocopy command lists /NC and /NJH twice.

$Folders and $Folder contain objects with properties, use these instead of treating them as strings (which implicit casts them as such) or pipe to Select-Object -ExpandProperty FullName
Same with $Files and $File 

I'd not reuse variable names but define neccessary ones from begin.
Proper indenting eases reading/understanding the code IMO better than excess white space.

The following script isn't tested at all, see it as rough template:

## Q:\Test\2018\08\12\cr_201527.ps1
Import-Module NTFSSecurity

$Logs  = 'D:\AutoAssign\Data\RoboLogs\'
$Final = 'D:\AutoAssign\Data\Final\'
$Folderpath = "G:\DEPT"

#Gets initial file and folder list
$Folders = Get-Childitem $Folderpath

ForEach ($Folder in $Folders) {
    Start-Job -ScriptBlock { Param($Folder,$Logs)
        robocopy "$($Folder.FullName)" NULL /L /S /NJH /FP /NC /XJ /NS /NJH /NC /NJS /LOG:"$Logs$($Folder.Name).txt"
    } -ArgumentList $Folder,$Logs
}

#Wait until all jobs are finished
Get-Job | Wait-Job

&lt;# functionality integrated into next sction
    #Trims out white space and empty lines
#&gt;

#Gets Owner for each file And Create CSV

ForEach ($File in (Get-ChildItem $Logs)){
    Start-Job -ScriptBlock { Param($Logs,$File,$Final)
        $OutputFile = Join-Path $Final "$($File.Name).csv"
        $Results = ForEach ($Path in ((Get-Content $File.FullName).Trim() -ne '')){
            $Owner = (Get-NtfsOwner $Path).Owner.Trim()
            If ($Owner -ne "BUILTIN\Administrators" -and
                $Owner -ne $null                    -and
                $Owner -ne "Domain\Domain Admins"   -and
                $Owner -notlike "S-1*"){
                [PSCustomObject]@{
                    Path = $Path
                    Owner = $Owner
                }
            }
        }
        $Results | Export-Csv -NoTypeInformation -Path $OutputFile
    } -ArgumentList $Logs,$File,$Final #Ends Initial ForEach

}  #Ends Job Script Block

#Wait unitl all jobs are finished
Get-Job | Wait-Job

#Merge all files into one CSV
Get-ChildItem  D:\AutoAssign\Data\Final | Select-Object -ExpandProperty FullName |
    Import-Csv | Export-Csv D:\AutoAssign\Data\G.csv -NoTypeInformation -Append

#Delete all original files
Get-ChildItem D:\AutoAssign\Data\RoboLogs | Remove-Item
Get-ChildItem D:\AutoAssign\Data\Final | Remove-Item