The built-in armor is only an advantage for the first few levels and quickly becomes a disadvantage after that.
The main reason is time. Fighter A, a dwarf, can commission a new set of armor and go off and do other things in the meantime. Fighter B, a warforged, has to sit there for the full amount of time it takes to enchant him. When you get to the mid levels and higher this is extremely onerous, especially in a campaign with a plot that actually advances with time.
In some of the games I've played, the WF needing to sit around for, say, 9 days (+3 armor) would have been a HUGE problem, because the world (or at least the neighborhood) would be getting blown up in the meantime.
Even in games where the DM allows time for crafting, there are often long periods of time broken up by occasional breaks; in those long adventuring periods, the WF can't upgrade his defenses; dwarf fighter A at least has the chance to find a nicer suit of armor in a treasure hoard.
On top of all that, the WF has to spend a precious feat on his starting armor, where dwarf fighter A just has to spend a renewable resource, gold, and will often have enough to get his own set of full plate (leaving only the DR as the difference) sometime during level 2-3.
This means, for example, that a WF fighter can't get cleave at level 1 if he wants to have a decent AC. He can't get both EWP (bastard sword) and power attack. Losing your second feat at level 1 to get a one level jump on armor ownership isn't a really great trade in my opinion.