[MENTION=10169]TheDurk[/MENTION] I didn't notice there were dowels and studs on that one. Definitely no need for the gorilla snot on that gasket. I used the water pump as the first thing I thought of. A lot of engines do have paper gaskets and nothing to really line them up. It works for plenty of other gaskets though. Just be smart about it.
As for concerns about making your own marks... Again you have to be smart about it. If you are willing to go this deep into your engine, you should be able to notice if it starts to run rough. If it's for a customer, ask if they have noticed a drop in mileage or power. An engine a tooth off is going to run like crap. If you bought it that way and suspect it was done wrong, check the timing... otherwise if it's just routine maintenance, marking the engine ensures that you don't end up off and it saves time.
As for the crank pulley, hopefully you know to remove that first before marking the gear. You have a point to check the keyway and pulley for any looseness or signs of wear.
Sometimes if you have to set the timing, the marks aren't very clear. Fortunately Toyota does seem to be pretty good about that. Unfortunately for me, when I was rebuilding my engine I didn't know how it ran (junkyard motor) so I set it to the factory marks. The dimple on the crank gear looked like the timing mark on the opposite side. I consulted someone else and the diagram, but we had a disagreement over which was the mark. I should have gone with the one I was going to use as it ended up 180 out. No big deal though.
I don't mind the debate by the way. I know I've only been doing this for about 3-4 years so I'm a n00b, but I have done at least 20 timing belt jobs that I can think of.