Out of the box Windows Server 2012 creates system folders System32 & SysWow64 and makes them owned by TrustedInstaller.
So you want to run the server as a Webserver and register your application DLLs on the server. In order to do this you need to create a website with an Application Pool that has an identity. So you can use inbuilt user ISUR or create a new user and make it part of the user group IIS_IUSRS group.
So you have a problem as you need to give ISUR or the IIS_IUSRS group Read and Read & Execute permissions on the System32 & SysWow64 but the machine Administrator is unable to do this.
First you must take ownership of these folders and replace the TrustedInstaller with the real machine Administrator. You can then grant access to the ISUR etc.
I am presuming that this is the only way you can setup a webserver or am I missing something? There is a lot of advice suggesting that taking ownership of System32 is not a good idea. But I cannot see any other way of doing it?