Taking levels as a Dragon Disciple does not give exactly the same effect as being a half-dragon in the first place.
That's not a particular surprise to me. In this case, I presume it's done out of a desire not to change hit die sizes retroactively. I mean, if you reroll those hit dice, can your total go down if you have bad luck? If it cannot, it's still not the same as if you were a half-dragon all along, because you're probability distribution is going to be skewed high. Or, instead of rerolling, they could give you +1 hit point per die on the preexisting hit dice, which is approximately the same number of hit points but once again, still not the same distribution.
So instead, they start you at d4 (typical for sorcerers, who are the target audience of the class) and increase that several times over the course of the level progression (whereas a half-dragon gets a flat one-size bump to his hit dice). Overall, by the time you're done, those exceptionally large dice will have made up a lot of ground for your pre-prestige-class d4's, but the end result is only approximately the same.
Actually, someone should run the numbers to see how the average hit points actually do compare between a 10th-level dragon disciple, who got the class as early as a sorcerer could be expected to, and a half-dragon sorcerer of various levels. I would if I had the book here.
