I'm the maintainer of Cantarell and the guy who pushed the changes in
FreeType. What you see is intentional:
http://freetype.org/freetype2/docs/text-rendering-general.html#slight-hinting-invokes-the-native-hinter-if-possible
Basically, we now try to use Adobe's native hinting machinery instead of
FreeType's autohinter whenever possible to make text fit for display on
low-DPI screens. A native hinter uses the information the designer put
into the font and is likely to produce a better result than the
(actually quite good) guesswork of the autohinter. Since both approaches
work differently, you may get different results at different sizes. The
most visible difference is that letters may be pulled up/down at
different sizes, which is what you see here. The pulling up at the
standard UI size was done by me.
If you don't like these changes, try inserting the following snippet in
your ~/.config/fontconfig/fonts.conf:
<match target="font">
<test qual="any" name="family"><string>Cantarell</string></test>
<edit mode="assign" name="hinting"><bool>true</bool></edit>
<edit mode="assign" name="autohint"><bool>true</bool></edit>
<edit mode="assign" name="hintstyle"><const>hintslight</const></edit>
</match>
This will tell toolkits to handle Cantarell the previous way (GTK3
honors it, others may not).