aplonis:

Changing the font size in a PDF file will cause you some problems unless you change the page size as well. If you don't change the page size, then you'll have to recompute the page layouts, or you'll have quite a messy PDF file.

Since calibre is apparently generating your PDFs, I'm guessing that it does page layout at the same time. If so, I'd suggest telling it the font size to use when generating the document. (Note: I'm assuming that calibre allows you to configure the fonts for PDF file generation.)

...roboticus

When your only tool is a hammer, all problems look like your thumb.