Here's the difference:
Bolts are ok obviously since Toyota uses them factory, but they're cheaper than the studs and easier to make so that's also why they do it. When you torque down a bolt the friction in the threads causes the bolt to give resistance, and that may lead to somewhat less accurate torwue readings. Example, you torque it down to 80lb/ft but it's really only 76 or 74 because as you tightenned it the bolt's resistance in the threads as you turned it made the torque wrench think it was tighter than it was.
Studs are better because you tighten it finger tight, so it's already tight before you even begin to torque it down, so this means the torque reading you get is more the actual clamping force on the head, and not so much the torque on the threads of the stud into the block, which isn't what you're trying to measure. Example, it'll read closer if not exactly what you wanted to torque it down to, assuming your wrench is accurate and properly calibrated.
eric