The only way to permanently remove deleted Modern sites is PowerShell. Let’s delete a site collection in SharePoint Online using PowerShell. I ran these commands from Administrator Powershell (please see attached screenshot and the 'Feb27TeamTestB') :
Get-Module -Name Microsoft.Online.SharePoint.PowerShell -ListAvailable | Select Name, Version
Install-Module -Name Microsoft.Online.Sharepoint.Powershell
Update-Module -Name Microsoft.Online.Sharepoint.Powershell
Connect-SPOService -Url https://xxxxxxxxxxx-admin.sharepoint.com -Credential xxxxxx@xxxxxxx.onmicrosoft.com
$DeletedSiteCollURL = "https://xxxxxxx.sharepoint.com/sites/xxxxxxx"
Remove-SPODeletedSite -identity $DeletedSiteCollURL -Confirm:$false
And after that the Site was now permanently deleted.
There's no way to permanently delete just the SP site and not the Team site.
And there's no way to be selective on what is deleted such as specifying to delete specific portions/ folders of the site such as deleting the pure Sharepoint-related content while leaving the leaving the Teams-related content.