Actually the difference in damage can be quite large in a 1 on 1 environment. It is only when you compare damage on an 8 man party scale does the damage difference get down to negligible levels. When your tanks are doing about 200 dps, a tank doing 50 extra damage per second is a 25% increase... but when your raid is doing 2,000 dps, adding the same extra 50 DPS isn't such a big deal (2.5% extra).

The other side of the coin is that WAR damage/threat is not the smooth curve that PLD damage/threat is. It is very spikey. Using damage cooldowns together will give you very large spikes in threat, ideal for letting your DPS players go nuts on the pull, rather than having to slowly ramp up for the PLDs more steady threat generation. This will help a lot on any fight where you are racing a timer, or once you have the fights on farm and are simply trying to clear the fights as quickly as possible.

The rest of what you say is true though, sadly.