Preventing email overload is definitely something we work hard to avoid. We know that if there are too many false positives people will simply ignore them.
And we shutdown the farm as soon as we diagnosed the issue:
http://status.ros.org/ Unfortunately when you run a very parallelized system if there's a systematic failure, such as the code hosting going down, a lot of jobs fail quickly.
One thing from travis testing Travis distinguishes between build/test errors vs configuration errors. There's a ticket open to add this enhancement
https://github.com/ros-infrastructure/buildfarm/issues/116 but unfortunately this is not something that Jenkins differentiates so it will take a lot of doing to make this happen on top. An approach I could see for this is to customize the emailing plugin and be able to pass it flags earlier in the process confirm that the configuration and setup has completed successfully. And likewise the actual results should be shown the same way too with the job aborting instead of failing when the configuration/setup phase fails.