Twitter had a comprehensive browser and system test suite that took about an hour to run (and they had a large CI worker cluster). Flaky tests could and did scuttle deploys. It was a never-ending struggle to keep CI green, but most engineers saw de-flaking (not just deleting the test) as a critical task.
PhotoStructure has an 8-job GitLab CI pipeline that runs on macOS, Windows, and Linux. Keeping the ~3,000 (and growing) tests passing reliably has proven to be a non-trivial task, and researching why a given task is flaky on one OS versus another has almost invariably led to discovery and hardening of edge and corner conditions.
It seems that TFA only touched on set ordering, incomplete db resets and time issues. There are many other spectres to fight as soon as you deal with multi-process systems on multiple OSes, including file system case sensitivity, incomplete file system resets, fork behavior and child process management, and network and stream management.
There are several aspects I added to stabilize CI, including robust shutdown and child process management systems. I can't say I would have prioritized those things if I didn't have tests, but now that I have it, I'm glad they're there.