Yes this should be possible with powershell on Windows Server 2016.
Commands obtained from technet (https://technet.microsoft.com/en-us/library/dn433280(v=wps.630).aspx)
Please see the below.
Set-MpPreference -DisableRealtimeMonitoring $false
Start-MpScan -ScanType FullScan
$Report = Get-MpThreat | ConvertTo-Html
If ($Report -ne $null){
Send-MailMessage -From <SenderAddress> -to <RecipientAddress> -SmtpServer <SMTPServer> -Subject "Defender Report" -Body $Report
}
Set-MpPreference -DisableRealtimeMonitoring $true
I can confirm that the scan works and the real time monitoring gets disabled, however as my WS2016 environment is clean I am unable to test the report.
This can be saved as a ps1 file and used in task scheduler.
Things that could have an impact is other anti-virus suites disable and prevent defender from being enabled, eset being an example.
hopefully this helps.