1) Instead of asking why the portfolio is equal to the premium, ask why create it at all? I say that because it actually isn't equal to the premium, since that would just be D, and also because the actual value isn't as important as what the portfolio represents.
We form this particular portfolio because the laws of no-arbitrage guarantee it has a certain rate of return (within a set of necessary assumptions). That gives us a constant point which we can exploit to solve the equation; without this observation, the equations aren't grounded.
Specifically, the portfolio consists of a short derivative paired with an amount of stock such that the change in the derivative price due to the stock moving is exactly offset by these shares. That amount, represented here by the $\frac{{\partial D_t}}{{\partial S_t}}$ term, is called "delta". Because of this pairing, the resulting portfolio is not exposed to risk (i.e. it has been hedged) and therefore we know it must return the risk-free rate. In a later step of the derivation, we will differentiate the portfolio value with respect to time and use this information to figure out what that is (unsurprisingly, it is simply a proportionate piece of the risk-free rate).
So in sum: the portfolio is set up in such a way that we know how it behaves, a fact which we later use to anchor the differential equation.
2) This equation is valid for any derivative that is differentiable twice with respect to S (the stock price) and once with respect to t (time). We have made no assumptions yet about put or call. As you will see, delta for puts is between -1 and 0, so if the derivative were a put the stock component of this portfolio would be negative.
Hull's book really does a great job of explaining this, I suggest you pick up a copy if you haven't already.