Hmm... All things being equal, the larger cooler should in theory allow for more flow, but if there is a difference in core design, or other factors, It could cost power going to A/M v/s the stock setup. (But I don't see very many ways it could do that allowing for the size area we have up front anyway.)
Fact is, even the stock CT-26 can flow plenty of air to fill up even the largest FMIC the Supra could sport. So even you if ripped the front bumper off, and mounted an intercooler from a MACK truck, it might increase the lag, but it would have less pressure drop across the core than the stock one in theory when your running a cooler designed for the airflow needs of motor that is 2 or 3 times the size of ours. (So, ultimate peak power might be higher due to the cooler charge, and increase from the loss in pressure drop across the core....)
That being said, I have a MAXX direct fit setup, supposed the flow fine up into the 750hp range, or better than 1000cfm of airflow with minimal pressure drop. (Or something like that.)
Best for flow are top/bottem tanks on our cars with the flow going up/down for maximum core openings, but most Ebay, and my own setup are side to side and your limited by the height/thickness dimension of the core that way much more than the top/bottem designs. (Read Corkey Bell's book on Turbo charging cars if you have more questions.)
Shorter pipes are good. Larger diameter pipes can increase lag at the gain of more flow. (But if they are much bigger than your throttle body, what's the point? Same goes for being much bigger than the exit of your compressor housing.... )
So with that in mind, when I made my pipes, I went 2.25" ID (Just slightly larger than the ID of the Compressor outlet.) pipe out of the compressor into 2.5" ID pipes and the IC that is 2.5" ID inlet and out, and then just before the throttle body, I have a 4' long 3" ID pipe section that feeds the throttle body. (My goal was to try and enlarge the plenum volume under WOT conditions, and the 2.5" feed pipe sticks into the 3" section about 8", so it's anti-reversion as well, and I have two 1" BOV's venting off this large 3" upper pipe, so it all worked out well.) I notice no increase in lag, and it seems to work well for the BOV's and other design parameters. The twin BOV's are Bosch, and leak under vac conditions, so they provide a shortcut to the TB, and bypass the turbo.. so better low end throttle response was the goal, and it seems to work fine...
Whew! sorry for the long post.