Hi,
In the free version of Tina-TI you can model transistors (no idea how complex or simplistic as that level is way beyond me) and even better, make block models to reduce whole circuits to IC-sized parts, it's pretty comprehensive, I am under the impression it can slow down simulations sometimes. You can create netlists, afaik.
All SPICE-based sim tools must have this option somewhere in a menu.
Imagine the details and time needed to make just a pcb track + solder joints (Seebeck Effect) emulate pcb hot and cold spots, and so on, give more realism to the simulation and results.
I think simulation tools are best-foot-forward approximations to mostly perfect realities, presumably idealized and unable to emulate an IC/a passive component/a board/circuit 100%: part-to-part variations, layout, operating environment, etc... and should be taken as accurate guides to component and circuit operation only.
Things are always much better, and sometimes fantastically misleading in simulation world, as you know - e.g. at the extreme end of unbelievable, I can make 1ppm voltage references from 0°C to 100°C with four resistors, two BJTs and one generic op amp
...