I summarized our new best practice here: http://tommyhallett.tumblr.com/post/37318050812/avoiding-ren...
As you point out, appending the element to the DOM before everything is fully rendered can cause all sorts of re-drawing to go on. When that's a concern, I proactively set height/width dimensions on the element before adding it. In cases where that's problematic, I just have the render function of the view either update or remove the explicit height/width styling. That seems to help avoid the worst cases of redrawing/flicker.
Another benefit to this approach is it makes replacing, disposing views, creating stacked views easy ... That is when renderTo tries to insert into a container and determines a view is already in place, it can call dispose or detach on the existing view. Much simpler than Marionette regions or other view management approaches.