I would position the directive between the scope and the template - in reality it is directives that interact with the DOM, not the scope (or controllers).
Also, since AngularJS is compiling DOM nodes not strings, there does not need to be such a difference between the "view html" and the "rendered html". Rather there is a compilation process that attaches AngularJS goodness to the DOM and then directives interact with the DOM directly. This happens throughout the application life-cycle when DOM nodes are added and removed dynamically by things like ng-repeat and ng-include.