First off, either I have misread the PrC or you have.
I've not got my books with me, however the PrC gives you an extra wildshape usage per day per level. So to begin with you are shapeshifting more often. This doesn't come into strength until Master of Druid 5/Many Forms 3 where you have 4 shifts a day as opposed to Druid 8 who has 3.
Secondly, the duration is 1 hours per level or something isn't it? And the Master of Many Forms levels stack with Druid levels for the determination of this. By Druid 5/Master 2 you have 3 shifts of 7 hours each (almost a complete day).
Next the Master of Many Forms starts gaining special abilities of the form he/she takes. So indeed the Master is a more powerful shapeshifter.
As to the HD limit, there are large creatures for example with low HD. Look at a Minotaur for example, 6 HD. A Druid 5/Master 1 has 6 HD as well so you can become a Minotaur without thinking. You can also shapeshift into an advanced version of a creature. So when you get Gargantuan you can become an advanced Minotaur if you desire.
D