How can I update a Sitecore XML patch file using SIF?

Okay, I got it working. The problem was with the inability of the SetXml SIF task to provide an XML NS.

So I created a custom task based on the SetXml task with an extra parameter to provide the namespace, the SIF configuration (in my case) then becomes as follows:

"SetDataFolder": {
      "Type": "SetXml",
      "Params": {
        "FilePath": "[joinpath(variable('Site.WebsiteFolder'), 'App_Config', 'Include', 'DataFolder.config')]",
        "XPath": "//configuration/sitecore/sc.variable[@name='dataFolder']/patch:attribute[@name='value']",
        "Namespace": [
          {
            "patch": "http://www.sitecore.net/xmlconfig/"
          }
        ],
        "Value": "[parameter('DataFolder')]"        
      }
    }

To accomplish this, just copy the complete SetXml task from the SIF library, make the necessary modifications to support the namespace in the Select-XML method, and include it in your module loading and be sure to register it using an overwrite of the out-of-the-box module using

Register-SitecoreInstallExtension -Command Invoke-SetXmlTaskEx -As SetXml -Type Task -Force

Hopefully this will help anyone else stumbling into the same problem until it hopefully becomes part of the official SIF version.