On a laptop with high DPI display, I'm using 6pt fonts in both KDE and GTK, plus ~/.config/Trolltech.conf file with following content:

[qt]
font="Sans Serif,6,-1,5,50,0,0,0,0,0"

Tried with all available versions of Qt Creator: standalone, with SDK, and distribution package, all of them are absolutely the same: looks like 12pt or similar font size is used as default. Didn't found any special configuration where default font size could be set.

Solved that by writing custom stylesheet (which is rather inconvenient, unless there is a possibility to set system default stylesheet which I'm not aware of) with following content:

QWidget { font-size: 6pt; }

After fixing size issue, it appears that fontconfig settings are not respected. At first I thought that it uses different font family ("Sans Serif" aliased to DejaVu Sans in the fontconfig), but looking more closely it appears that it uses another hinting level - fontconfig is configured with hintstyle hintslight, while Fusion uses either hintmedium or hintfull (compared main menu with KWrite main menu, in QtCreator all letters are narrower and more fitting to pixels).