I have inserted numerous links to a text I created on the demo site. However, when I go to "publish" the book and view it, the links do not have the standard blue color that links usually have. So, you can't even tell that they're clickable links.
I went in and manually tried to format them with blue font, but it still won't show.
PDF is styled using CSS, just like web sites are. For instance, on Demo site links are forced not to be underlined and in black color. I don't know how much you are familiar with CSS but this is for instance style for links "a { text-decoration:none; color:#000;}".This can easily be changed and if you have your own installation of Booktype (or use Booktype Pro) you can style all of your books in the same way.
With CSS you can easily add border or shadow to your images, change padding, spacing, style your headings in different way, change fonts and do many other things.