I don't know the solution to your problem with certainty.
I believe the answer has to do with hinting. Full hinting yields thin font strokes, while no hinting yields thick font strokes.
Hinting can be set in at least 3 different places and I'm not sure how these settings interact.
The first place to set full hinting is by clicking on System>Preferences>Appearance>Fonts tab>Details.
The second place is to edit or create a file called ~/.fonts.conf and put this in it
If you do "man 5 fonts.conf" you'll see that Fontconfig reads this file.
<!DOCTYPE fontconfig SYSTEM "fonts.dtd">
<match target="font" >
<edit mode="assign" name="rgba" > <const>rgb</const> </edit>
<edit mode="assign" name="hinting" > <bool>true</bool> </edit>
<edit mode="assign" name="antialias"> <bool>true</bool> </edit>
<edit mode="assign" name="autohint" > <bool>false</bool> </edit>
<edit mode="assign" name="hintstyle"> <const>hintfull</const> </edit>
The third place where hinting can be configured is /etc/fonts/conf.avail. These, I believe are system-wide font configuration files. I don't know enough to say with confidence how to edit these files, but if you look in /etc/fonts/conf.avail/53-monospace-lcd-filter.conf you might see something like
Which I think means that monospace fonts are rendered with full hinting by default.
<edit name="hintstyle" mode="assign">
So maybe if you set all hintstyle to hintfull in all three locations, maybe emacs will get the message.