I have installed a tool for desktop and background 64bit processing on window server 2012r2 with arcgis 10.3 and I haven't problem so I don't think a bug. Seems that esriregasm cannot write the file reg in your directory.
Have you tried without filename ("... This only works with managed assemblies, and the generated .reg file will not contain any category information. If the file name is not specified, by default, it is generated in the same directory as the assembly and has the same name as the assembly with the .reg extension (optional)....") ? /regfile