I think "playing with antialiasing" (in GNOME) should be the same as setting Use antialiasing: true, then going into Configure, checking Use sub-pixel rendering (RGB), and selecting Hinting style: Full. Beware that it *will* recreate your current ~/.fonts.conf file and flatten your hierarchy and neat comments, so back it up first.
Those fonts settings (at the wiki page you linked to) add quite a bit of complexity, so I'm not quite sure what's happening to your Arial. It doesn't look like Arial to begin with, and it seems to only have light hinting, or perhaps it's being auto-hinted.
To begin with check if it's being mapped to something else.
Code:
$ fc-match Arial
Arial.ttf: "Arial" "Normal"
Aside from that I'd just try to selectively comment sections out of the .fonts.conf file and iteratively track down what could cause the behavior. Changes will only affect newly started programs.
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