Does the MainWP Add-On work with Multisite?

Yes, technically it works fine in Multisite, you could even activate it Network-wide if you want. However, it makes absolutely no sense to setup a “MainWP Dashboard Site” as Multisite install!

Such a “Dashboard Site” is for managing dozens of other websites and therefore should be absolutely lightweight and only focused on this one purpose. I would only ever recommend to run the MainWP Dashboard on a regular single WordPress install, which is also fine-tuned for security and performance, plus, completely locked-down for the public.