Hey John,
Welcome to the forum, thanks to you for using Speckle and for the feedback! 
Feel free to Introduce yourself 🙆 if you’d like!
Speckle and Rhino Inside are definitely a great combo, how you use them really depends on what you are trying to achieve. If you can elaborate more the “automatic querying Revit files with custom filtering logics” we will try to suggest something.
With your second question, I’m not 100% sure what’s going. If you could share a link to the stream with the Grasshopper door mesh I’ll have a look. My assumptions are that it might due to how Rhino inside extracts data from Revit, or simply it could be a bug with our Expand User Data component.
You don’t need to create a Speckle Object to send the mesh since it’s a supported data type, you should be able to send it as it is via Speckle.
Also, we’re slowly deprecating Speckle v1, in favour of the upcoming release of v2 which will have a much improved Revit integration and better Grasshopper nodes, stay tuned!