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Your output doesn't show any failed packages - only packages which printed to stderr:

Summary: 226 packages finished [1h 12min 39s]
  8 packages had stderr output: ...

Without the actual output being shared I have to guess: the Connext-related packages likely print a warning that since Connext is not available they will not provide any functionality. The very same for the OpenSplice-related ones. And for the ros1_bridge since you didn't have ROS 1 sourced the warning message lets you know that the bridge is being skipped.

Therefore the resulting installation should work fine using FastRTPS.

I am using a second overlay workspace which fails to build because the main ros2_ws does not provide a correct source.

I don't understand what this means. Please descibe in more detail what fails and what sources you expect which you think are missing.