I just installed Safari 10, and I'm not really sure if the font size has gotten smaller or not, but it seems like I'm now seeing a brighter screen (Is it possible?), and if the font size is smaller it's unnoticeable to me.
I poked around a bit to see if Apple has moved the font size pref, and I didn't find it.
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In Memory of Harv: Those who can make you believe absurdities can make you commit atrocities. ~Voltaire