I'm seeing this already with how they're handling the new right-click contextual Search feature being moved to open the results in the new "Search sidebar" rather than a new tab. This was supposedly able to be disabled with the flag "Search web in side panel" (there's no option for it in the preferences), however if the completely undocumented "CSC" flag was left at it's default then it overrides any other flag to force enable the feature. You can see the consequences of this decision to this very day in places like /r/chrome with users complaining that disabling the feature flags isn't working.
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