First of all, let me point out that the master branch is not up-to-date. My report refers to latest version of plugin which uses feat/ns7 branch of this repo.

For few months now, NativeScript CLI has got --config parameter which allows you to define a path for a custom nativescript config file.
I removed old nativescript.config.ts and created a new one outside app root directory.

Usage example:
ns build android --config="../../myconfig/nativescript.config.ts"

So far so good. On the other hand, @nativescript/hook plugin will decide if current directory is the app root one by checking if nativescript.config.ts is present. For those who use a custom file inside another directory, this will be a problem as file will be missing.
As a result, my hooks will not be generated if I don't keep an empty dummy nativescript.config.ts inside my app root directory just to make sure _isNativeScriptAppRoot returns true.

This method decides if given directory is app root directory by looking for nativescript.config file.

function _isNativeScriptAppRoot(dir) {
  var tsConfig = path.join(dir, 'nativescript.config.ts');
  var jsConfig = path.join(dir, 'nativescript.config.js');
  if (fs.existsSync(tsConfig) || fs.existsSync(jsConfig)) {
    return true;
  }

  return false;
}