The trade off is in relevancy. If the standards body doesn't force a confrontation it knows it can't win, then it retains some power that it can throw behind or against future proposals. If the major browsers have already decided to completely ignore them and create their own consensus, there's that much less reason to listen to them next time. Not only has a precedent been set, but coordination on features outside the control may have already been somewhat standardized behind the scenes (beyond what they already do), making it easier next time.

The downside is as you say that the browsers can point to the standard as for why they implemented it, but that's why it's a trade off, and not cut and dry (IMO)