"if I want to rebuild a server all I need to do is a clean install followed by apt-get/yum install and then in the vast majority of cases you simply copy a configuration file over from the old machine"
Even easier on Windows Server - you can use Restore Settings to return it to a clean install state.
"With the registry in place the configuration part of any particular application is disconnected from the application itself and placed into a binary blob that is impossible to copy"
Which is far more sensible / scalable / performant than flat text files. They are not impossible to copy - configurations can easily be exported to text and can then be imported.
"MS Office, is peppered throughout the registry instead of residing in its own "branch" of the tree and is therefore mixed in with all the configuration details of all the other applications in the system"
MS Office has its own application configuration "branch" in the Registry. Well a couple - one for the machine specific config and one for the user specific config.
"Further obfuscation is achieved by "hiding" binary stuff (ie "non ascii") "
It's generally not hidden at all. You can view it as ACSII and / or as hex values.
"and borking the registry editing tool so that it will not allow you to even see the "non ascii" parts let alone edit them"
You can view binary data. What this Malware has don't is changed a KEY NAME to be non ASCII which is not supported - and therefore not visible in the editor utility. There are other tools to let you see this sort of corruption / error and remove it.
"the only possible way to install something now is to go through the complete install process"
Nope - you can install something manually if you really want to. However I cannot see any reason to want to do so versus using Windows Installer. Which is very powerful and is far superior to any Linux installer I have seen to date.
"which requires access to install media and the associated DRM hoops that must be jumped through."
You generally only need the MSI file. Office doesn't require any actual "media". The only DRM is the license key check. There is no DRM control over Office install executables and media.
"There is absolutely no valid reason that a product like MS Office requires such a ludicrously complicated and widely dispersed configuration other than as a means for Microsoft to create such a complex mess of details so as to make using illicit copies of their software more difficult."
Utter bollocks - as above the configuration is not in general 'widely dispersed' and that configuration location has nothing what so ever to do with the way the Office copy protection works.
"you really should not be commenting on stuff you know nothing about."
Pot, meet kettle.