If their animator request is to be taken literally, they’re using Spine, which is not a pixel art tool but is used for a hybrid of 2D animation and tween-style deformation of illustrations. It’s used by Size Five games (the latest Ben & Dan game for example) and can produce output similar to the animation in Broken Age.
I’ll be clear here that I’ve never used Spine and don’t know all the contexts in which it’s used, but it’s definitely a general purpose 2D animation tool.