The difference in power you might gain is due to tuning/adjustments.
While what your dad said is true, there is an optimal balance between power and fuel economy. Take for example the Altima and new Maxima. As marketing goes, they decided to keep the Altima at 270 hp, and to get more power, you gotta pay more for the Maxima, if you want 290 hp, out of the same engine, and pretty much similar exhaust/etc. layout.
In fact if we follow your dad's logic, then Nissan should already include a better y-pipe, and cat-back exhaust. But they don't because the stock setup is tuned more so for daily driving, which is usually 1500-4000 rpm range, where the engine spends most of the time and so is tuned from the factory to have more available torque there. With larger diameter exhaust tubing and aftermarket y-pipe, you are sacrificing some low end/rev torque for high RPM performance. Again it's all a balance and Nissan takes the average non-boy-racer to be the overall customer and driver.
The GT tuner takes the curve of power and economy and tunes it toward more power by giving the engine more/less fuel depending on rpm/load and so you get more power, at the cost of more fuel usage perhaps. I too don't know the exact details, but that is a simple way to explain it.
Any exceptions I can't think of aside, the Maxima and Altima share the same engine as far as I know (as in parts used etc), and are only really different in their power ratings and fuel economy due to tuning. If it were up to the consumer we'd all want our Altimas to cost $26k and come with 300 Hp like the anniversary edition 350z did for a while....with pretty much the same engine with a few hotter parts, and tuning.
I've actually been looking into getting a tune done to my Altima from Uprev to get any extra juice I can from the stock engine of mine, having already added a cat-back exhaust and aftermarket y-pipe to improve exhaust flow. Maybe I could reach or breach the 300 crank horsepower rating (stock being 270), and reach the same level of performance of an older 350Z, without spending 4 grand?....

Wishful thinking? Maybe not. The tuning service costs about $500+ but unlike the Bullydog, which only has a generic template to increase hp, the custom tune would properly take into account my aftermarket parts and other variables to get the most out of it, safely.