So ..... Toyota didn't invent a new "type" tank or fuel pump for the LC, of course the tank is a different shape than others because it's a new frame/body and the available space is different than other models.
A fuel injected engine is a fuel injected engine, whether port injected, direct injected or both, nothing special about that. When the ECU calls for fuel, it turns on the fuel pump and turns it off when it doesn't. How often this happens has nothing to do with fuel tank or fuel pump but how often residue fuel is returned to the tank (diesel is a different story).
If you read the warning in the manual about being "pressurized" , you are correct about the EVAP system, just like every other fuel injected vehicle. Most probably put in there along with many other warnings so that Toyota wouldn't be liable for the idiots out there waiting to sue because they inhaled gas vapor.
The fuel pump for the LC has the same part number as the fuel pump for the GX.
So the limitations as I see them are; the physical space available in the LC vs the GX and the physical location of the fuel pump, relative to the frame, on the LC vs the GX and is why the GX fuel lines were ordered (hopefully won't be needed).