I can help on the toilet! The 12" is from the finished wall to the center (bolt holes) of the toilet flange. The offset for the toilet water supply does have a standard, but is dependent on whether you have a standard toilet! FOr example, I've installed several Toto models (highly recommended) that require the water to be further from teh center line than "normal" because of the shape of the fully faired base.
As to the other stuff, the supply lines for say a sink should account for the fixture that you are going to use - say if the faucet has attached lines, you don't want to have to try to extend then, and you don't want them looping all around. Also, you still want to be able to get to them, so you don't want them too high up, either. SO, while "normal" has its place (and the toilet flange is one that is pretty much truely standard for the vast majority of items), it sometimes depends on the actual stuff selected.
For a shower valve, if the owner was 6'6" tall, you'd want the shower head higher than normal (or adjustable), and you may want the valve higher, too. For a tub/shower combo, if you wanted to adjust the thing while sitting in the tub, you wouldn't want it too high. The tub filler needs to be a specified height above the rim of the tub, but other than that, some like a waterfall, even ceiling mounted!
One of the pros can probably give you some "standard" values, but I've found there is a lot of lattitude, and standard may not work with the specific stuff you select to install.