Selecting different font sizes allows you to control how the puzzle appears in the final format. With the "Printable HTML", the web site doesn't know how big a printer page is, so the user needs to make choices that make sense.
The "Printable PDF" is somewhat different. In this case, we make the puzzle with phrases as large as possible, but still fit onto a page. In the PDF format, we do know how large a page is, so we can make those estimations. The relative font sizes you select here control the relative sizes of the puzzle and word list. But two different puzzles with the same font size selections may have different character sizes because the puzzles have different numbers of phrases.