I wouldn't be too worried about the rust on the exhaust and other machined surfaces. The exhaust is bare steel so will naturally rust and the machined surfaces are areas that won't be painted, because it would create an interference with close fitting parts.
For peace of mind though, you could always just paint over the areas with some kill rust paint (not the exhaust obviously)
The main area to watch out for serious rust is the crossmember under the radiator. There is a strip of foam here to help seal around the radiator. Water gets trapped and rust the crossmember out quickly.
I have an '05 hilux and this crossmember is nearly rust through
The good news though is that the crossmember looks like it wouldn't be too hard to replace.