Ok, just checked through all the flattening preview highlights and everything looked fine in that. Since my exported document looked perfectly fine in acrobat, but sort of pixelated in mac's preview, is there any way around that?
If you are serving the PDF via a web address it will very likely be viewed in a browser (not downloaded and opened in an app like Preview or Reader). All of the browser displays have slightly different anti-aliasing, which you can see if you zoom in on a screen capture of the text. Here's a line of text from your PDF at 100%, magnified to 400% in Photoshop. From top to bottom Safari, Chrome, Firefox:
There's nothing you can do about the anti-aliasing quality of the different browsers and apps. The PDF you posted has live transparency, so it isn't a flattening issue.