As a site collection administrator, you can specify for each site collection if SPD should be enabled or not from the site collection administration page in each site collection.
/_layouts/15/SharePointDesignerSettings.aspx
So if you really have to enable SPD for just one site collection, i would use PowerShell to loop through all the site collection and disable SDP and then enable it for the single site collection where you need to use the designer.
Add-PSSnapin microsoft.sharepoint.powershell
$webapp = get-spwebapplication http://yourwebapplication
foreach ($site in $webapp.sites)
{
$site.AllowDesigner = $false
}
And then you can set the single site that you wanna use.
$site = get-spsite http://yoursitecollection
$site.AllowDesigner = $true
Update
To re-enable SPD on all the site collections again, simple just run the first script again but change $false
to $true
Add-PSSnapin microsoft.sharepoint.powershell
$webapp = get-spwebapplication http://yourwebapplication
foreach ($site in $webapp.sites)
{
$site.AllowDesigner = $true
}