Yes, the fly thing is odd but it is also possible to have an elasticated waistband and a fly. Looking at the picture you made of the instructions, I can see that the waistband was cut all in one piece so it is probably intended as a front-opening garment.

Hint: the back of a pair of pants always has the bigger crotch shape and is generally bigger ;)

Yes, the curve should be scooped out more for a larger bottom but the best suggestion I can give is to buy cheap unbleached calico, wash it and cut out a new pair of pants . Put it on inside out and make adjustments, using pins. Then, tack it together and recheck your fit. If you are happy take it all apart and then you have your very own template for a pair of pants that you'll be happy with in every way. Now you are ready to go and spend on fabric.