The manual is not usually included in the cost of PADI certification, as many people get them beforehand. It is however required by PADI that each family group should have a manual between them (no need for one each). At present in Belize you may find no manual is available to purchase anyway, as there is a severe shortage.
Other costs are usually all included, including PADI's registration charge of US$30. Not always though - ask. Similarly GST of 10% should be included, but you may find some operators adding that as well. The other improper charge that is quite often added is a %age for using a credit card.
I agree with Elbert about the great desirability for students to do as much book work as possible before they come to Belize. But PADI's eLearning is only one way to do this, and in my opinion not the best way. I prefer people to buy a PADI manual & their videos locally and study them to a programme I give them. It's cheaper overall than eLearning and they get their own paper manual to keep/write in as they will. With eLearning you don't get a manual.
You say you don't want advice on choice of dive center. For what it's worth, I know three operators on CC (I don't know a fourth...?) and I would have no hesitation in recommending Belize Diving Services over the others. A highly professional outfit.