When converting with calibre on the Look and Feel page you can also uncheck the Disable font size rescaling option then use the Base font size and/or Font size key options. You just have to play around with the options to find which settings work best for you. It is a bit more complicated since Sony changes text size when you switch from portrait to landscape, but it is still workable.

I think, but I'm not sure, that once you find the best settings for your tastes and save them as the conversion default, it will apply them to every book you convert and this will override the CSS in the books. Some changes that are made via conversion depend on whether and how much hardcoding was done in the book's CSS. Some books just use default font sizes by not defining them in the CSS, while others have defined font sizes for various divisions, elements, classes, etc. It is impossible to tell unless you look at the CSS.