Welcome to the forums, @jas89 !
The BOND team has indicated it could be done, but would have a lot of caveats and limitations, so it is not currently a feature they have enabled, nor do I get the impression that it is actively on the roadmap.
As far as the “Tracked State” on the fan – here’s a thread asking similar questions where Chris Merck from the BOND team considers various options - but I don’t think I’ve seen any of those make it into the current implementation, or at least not with any devices I have.
Overall, both issues you mentioned above are why I’m such a big fan (haha) of always hiding the OEM remotes for BOND (or other controller) linked devices which are toggle-based. If they have a discrete ON and a discrete OFF command, I can grudgingly let them stay out.
But if you take away the OEM remote, you’re forced to use voice assistants or the BOND app only – that is, unless you’re open to using other physical things like switches and / or remotes. Unfortunately, most of those strategies will require a more robust central smart home controller.
As an example, though, I have an ISY controller from Universal Devices which I integrate with BOND Bridges, BOND Sidekick remotes, Insteon switches and remotes, Logitech Harmony remotes (and many other devices).
My home’s OEM fan remotes are all tucked away in drawers, and each room has a BOND Sidekick or Insteon (sometimes plus a Harmony) remote and/or Insteon or Z-Wave switch that issues the commands for speeds, lights, etc via BOND’s API integration – and thereby each fan-and-light-kit keeps in sync with BOND.