It isn't uncommon to leave a box around the areas where the tub and shower drains will go so you have some flexibility in installing the drain and having a chance it will align with the fixture you choose. You need accurate plans to determine a toilet install. If you use 4", you can pour the concrete right up to the pipe then cut it off and use an inside flange. If you choose to use 3", then you need to sleeve it so you have room to slide the flange onto the outside of the pipe. The toilet pipe needs to be blocked so it is vertical during and after the pour after finishing the concrete, or installing the flange will be a pain. Exact placement of the toilet pipe is important, too, as if it is off a little, you'll either have a large gap behind the toilet, or have to use a non-standard one, limiting your choices and maybe increasing the costs.