Now that both tools are under the Boris FX umbrella and the Mocha tracking option is included in Silhouette, it is a good question.
If you use Mocha for roto, there are certainly similarities and you will find Silhouette has been optimized for in-depth roto projects. Beyond roto, Silhouette also has amazing paint tools (check out the detail separation) and a node based composting interface. So while Mocha might be used for tracking or roto “to complement a host” application, Silhouette has many more tools to finish shots.
For roto a few highlights from me… but I’d love to hear from more Silhouette users here:
Larger projects - Silhouette is optimized to handle hundreds of layers and will not bog down. Grouping layers and all that goes with layer management is something that is more efficient in Silhouette.
Tools not found in Mocha: Inverse Kinematics, Reshape + Magnet mode, B-Splines, ability to do more with open-splines, new RotoOverlay tools with moblur and onion skin, channel viewers, and more.
Also a big workflow feature for roto, Silhouette has multiple matte and keying tools, so a user can combine spline-based roto with various keyers to reduce the manual work.
This is my shortlist, but there is a lot more. Internally we feel that for large scale roto projects where you are working on the same project for many days or collaborating with a roto team, Silhouette is the tool of choice, however, if you are a compositor or editor and want to jump in and do some roto/masking than get back to your host application, Mocha Pro will prob work better for you.
I hope this helps. You can also find a comparison chart here: https://borisfx.com/products/silhouette/#compare