Technically, you agree with Microsoft, not the other way around. Also, I don't see what the big problem of chocolatey installing where it does. Cygwin, MinGW, Python, Ruby and others do it, too?
The default is in c:/chocolatey/. Oddly, chocolatey agrees with me. You are welcome to change that in your configuration, however.
The default is in c:/chocolatey/. Oddly, chocolatey agrees with me. You are welcome to change that in your configuration, however.