Specifically where do applications get their default font settings?
Regarding location of fonts, they are stored in /usr/share/fonts/ and /home/USERNAME/.fonts/. This may be somewhat relevant.
There is also a font section in the unity-tweak-tool for altering default font settings. Maybe give it a try.
The solution I've found is to edit the dpi settings in ~/.Xresources, by editing the line below to have the correct dpi value. The font now renders as it once did across multiple applications GTK or otherwise.
Xft.dpi: 96