I've used GWD, but personally, feel limited within the IDE. At least it's limiting when working with some of the designs that are passed on to me for development.
At the moment I'm working out a Gulp.js build system for banners that will allow tackling banner development using methods closer to a MVC approach.
To better answer your question though: I avoid the hybrid approach. Mostly out of concern that it is going to lead to bloated output, primarily on the GWD side.
As far as the application of GSAP animations to DOM elements is concerned, I keep all animation calls in its own self-contained layer. Unfortunately, due to legal restrictions I don't have anything that I currently share. I'll get something shareable pushed up to BitBucket sometime in the next week.
Here's the overall anatomy of an HTML5 ad built for upload in DoubleClick Studio:
index.html - ad markup, Enabler and Studio component init calls
ad.css - Ad styles. Also, if you are using webfonts that are not CDN hosted, optimize them and embed as a data URI.
ad.js - Contains the meat of your Enabler logic (Reminder to make initial Enabler component calls in index.html to make sure Studio detects the components)
animLayer.js - Contains all GSAP calls.
dynLayer.js - Optional - Contains all special logic for handling data used in Dynamic Ads.
That's my current setup. Once the Gulp build has been completed, all JS files will be aggregated and minified into a single script file.