There are still some significant differences... but lets start with Torque. First off, the Toyota Sport model (bigger turbo) has a max torque rating of 412 Nm (that's 304 ft/lb), so you CAN swoop up the engine to produce more torque (there is even a twin turbo version making 645 Nm called the 1KD-FTE).
And speaking of torque, it is important to note WHEN you have the torque available. If you look online, the Cummings torque curve looks like an inverted U, which means that while max torque rating seems higher than the standard Toy's, you only have that max torque available for a brief period, whereas in the Toy, you have that same torque for a wider range of rpm (from 1,800 to 3,600 in the fortuner, but depending on the setup, you can lower this range to 1,400 to 3,200, as it is in the HiLux).
The other thing you have to look at is weight. The 4BT is a heavy engine (well, ALL diesels are heavy because of the thick walls in the block required for the high compression ratios) even for a Diesel. I do not have the specs at hand for the Toyota, but it is a lighter (more modern) engine. Also, because the engine is more modern, you have better fuel economy, not that this will matter much to a trail rig...
I would also guess (I do not have the dimensions of the Toy engine) that the toy engine is smaller. You WOULD need to find a place for the intercooler, though; in the Toy's, they have a scoop on the hood for this purpose, but I guess you can probably fit it between the grill and the radiator.
Being in the states, though, I cannot recommend this engine; you will have a very hard time getting parts. Anywhere else in the world, it would be a completely different story, though. There is a reason Cummings engines are much less popular outside the US compared to German or Japanese engines...
Felipe