So i have tried TemplateB and TemplateA and both have an issue when pressing F5 to build, they both report the following error

System.IO.FileNotFoundException was unhandled
Message: An unhandled exception of type 'System.IO.FileNotFoundException' occurred in mscorlib.dll
Additional information: Could not load file or assembly 'Hspi, Version=1.3.101.0, Culture=neutral, PublicKeyToken=null' or one of its dependencies. The system cannot find the file specified.

so this is because the reference dll's are being copied into the
$(ConfigurationName)\bin<AssemblyName without "HSPI_"> folder
as per the fix-output.ps1 script, however the program cannot find these references there. if i move them back to the $(ConfigurationName) folder then all works fine.

why are you moving them? and where are you specifying that that directory is used to locate required references. BTW i am developing on a separate machine to where HS3 is installed and using VS2015 Update 3