In PDF's, the manual indicates that using different font sizes may (or may not) make the note function(s) not work properly. How about if you zoom the PDF? It seems like a lot of the two column journal article kinds of PDF's would lend themselves reasonably well to zooming, reading the first column, then panning to the second column, etc. But I need to be able to take notes at some point in there.

The zoom feature has different touchscreen commands in order to facilitate panning and dragging, so you can't take notes while the zoom is activated, or turn pages either. You can take notes with the font size enlarged though, but they remain on whichever size you make them on; it doesn't re-size your writing. Instead, a bookmark appears in the corner for the notes.