I will attempt to explain this...
forget the flange as a tell-tale. Mr Mitsu is right in saying there are two T4 flanges, but I've only ever seen a "T4" flange in one size - Garrett makes some T4 housings with a T3 flange, so I suppose you can say the T4 has two flanges available, T4-sized and T3-sized! Seems confusing, and it should, so don't worry abou that for a few seconds, and lets look at the important stuff... GAS FLOW!!!
(all the quoted numeric data is from the 2002 Turbonetics general catalog)
T3 stage 1 = 1.918" exducer, 2.319" major (a true "T3" turbine)
T3 stage 2 = 2.122" exducer, 2.559" major
T3 stage 3 = 2.229" exducer, 2.559" major (T300 turbine?)
T3 stage 4 = nonexistent
T3 stage 5 = 2.439" exducer, 2.798" major (T350 turbine?)
T4 N trim = 2.071" exducer, 2.922" major
T4 O trim = 2.296" exducer, 2.922" major
T4 P trim = 2.544" exducer, 2.922" major
T4 Q trim = 2.693" exducer, 3.111" major
phew!
ok, so keep in mind that a T3 exhaust housing is sized for a T3 turbine, and a T4 exhaust housing is sized for a T4 turbine...
also, keep in mind that A/R is a relationship between area and radius; saying "0.63A/R" does not imply a capacity to flow any particular amount of air, because it only defines the relationship between area at radius for that housing.
lets get back to the numbers...
If we take the T3 turbine major diameter to be 2.32", then the maximum cross section of a T3 0.63A/R housing can be worked out quite easily.
(2.32") / 2 * 0.63 = 0.731 square inches max.
If we take the T4 turbine major diameter to be 2.92", then the maximum cross section of a T4 0.63A/R housing can be worked out quite easily.
(2.92") / 2 * 0.63 = 0.920 square inches max.
So, for a given A/R RATIO, the actual flow area depends on the design of the turbine/housing family as well...
(incidentally, a 0.63 housing is not available for a T4, but a 0.58 is)
The other thing to consider is the turbine circumference. A T3 @ 2.32" has a circ. of ~7.29" inches, while a T4 @ 2.92" has a circ. of ~9.17" - this means the gas will flow through a longer path with the T4 turbine for the same turbine RPM when compared to a T3; the flow path for a T4 turbine is ~25% longer than the flow path for a T3 turbine. This is a bit of a generalization, because the air is directed away from the circumference by the turbine blades, but at low engine speed (when there is insufficient energy to really spin the turbine with some enthusiasm), all of these things are factors to consider because they all affect spool characteristics. You could get a turbine housing with the same cross-sectional area for a T3 and a T4, but the T4 would spool a little later due to the longer scroll length caused by the larger circumference. Now add to mix the increased leverage on the shaft provided by the larger diameter turbine wheel, and it should spool quicker because there's less load? well, maybe, but that's going to be very hard to prove or disprove. What about the fact that the larger diameter turbine will be more capable at trying to muscle around a large diameter compressor wheel (like say a T61?) when you start trying to crank up the boost?
...all of that numerical nonsense gets thrown out the window when you get to some critical RPM though, and the T4 makes WAY more torque than a puny little T3 could ever make because the flow paths involved with the T4 are so much larger than those in a T3... hit 5000rpm in a T4 and tell me why you'd want a T3? (I suppose "driveability" is a valid reason, and you will undoubtedly get better driveability and response from the smaller T3 setup)
blah blah blah
I'm losing my train of thought here, so I am bowing out - I hope you can gain some insight from my babble