Optimizing filament usage/transitions is definitely something we think about constantly. While we don't want to constrain people's design processes, there are ways to optimize designs for printing with Palette to reduce filament usage during transitions.
Because the same amount of filament is required for each transition, the percentage of filament used for transitioning is a function of how much filament is used on each layer of the print. So larger, flatter objects require less material to transition as a percentage of the whole print. Including multiples of the same model during a print also decreases the percentage of filament required for transitioning, as there would only be a maximum of 3 transitions per layer.
We've also considered transitioning in infill of the model, but things can get really complicated. We want the process of using Palette to be as simple as possible, and when we get into things like transitioning inside a model, it requires people to know things like filament show-through tolerance, opacity, contrast, etc.
For example, let's say we're printing a panda with black and white filament. It's very hard to know how thick the white shell needs to be to hide the black/gray/blended infill properly. As another example, if a model gets skinnier as it prints or has a lot of small diameter shapes, it would provide less room to transition in infill. For simplicity, we just transition everything on an external body. We haven't entirely written off transitioning on the inside yet. We just haven't yet found a way to make it simple.
You can learn more about Palette's transitioning options here.