This is getting really confusing, that's why I was trying to sum it up.
I believe there are 4 different issues here:
1) Gnome terminal and firefox not rendering like other apps when medium hinting is used
2) OpenOffice not using fontconfig settings : bug 54776
3) Fontconfig settings conflict between ~/.fonts.conf and Xft resources which result in different font rendering in some apps (same as 1) ?)
4) bug 60760, which is a problem selecting between autohinting and native hinting. no one talked about this issue here, and no Xft resources is used for this option, so it isn't the same as 3)
Please only talk about 1) here, unless you are able to identify duplicates in the above 4 issues.
Maybe a bug should be opened for 3)