Yes. When "text" mode is selected the contents of the text window are copied in their entirety between a \begin{document}...\end{document} pair. Hence, any arbitary LaTeX or AMS-LaTeX environment can be used in "text" mode. To typeset an aligned equation, simply use the appropriate environment:
\begin{eqnarray*} f(x) &=& x^2 - 4\\ &=& (x-2) (x+2) \end{equnarray}
This is a much harder question to answer than most people think it should be.
Mathematics requires many more fonts to typeset correctly than ordinary text. As a result, there exist very few sets of full math fonts. There are essentially six choices for TeX:
The PDF display routine relies on code from NSImageView, one of Apple's
Cocoa classes. The clipping is a bug within NSImageView. It shouldn't affect
the appearance of the PDF when dragged into Keynote or other applications. However,
it if bothers you, add a couple of points to the bottom margin of the bounding box
in the Preference pane.