We haven't tried the Avoidance stack in a while, so it's probably going to come down to what you are more comfortable with. If you are comfortable with Gazebo, SITL might be a good way to go.
The trick with ROS always comes down to making sure all of the nodes are talking to each other. There is a good tutorial on debugging ROS here
You'll want to have a list of the ROS topics the Ubuntu PX4 Avoidance stack requires, and then a list of the ROS topics the yocto base layer is providing. Then you'll need to map the two together.
You should only have one roscore, which should likely be in the Yocto layer. Your PC implementation should be able to see that if you have ROS_IP, etc configured properly.
The most valuable tool right now will probably be rostopic list and rostopic echo. Run ros topic on each of the layers:
- yocto base layer
- Ubuntu Docker
- PC workstation
Make sure you see the proper topics in each location and that they are publishing data.
Regarding stereo, I don't think that PX4 docs section is applicable. That RosDfsExample node should already be publishing a disparity map and point cloud. You can see it is publishing the disparity map here and point cloud here