Currently the ${\textsf{\color{red}/config/mekanism/Mekanism.cfg}}$ "tier" and "usage" sections are ones the game is using.
${\textsf{\color{red}/config/mekanism/Mekanism.cfg}}$ "-tier" and "-usage" sections can be deleted, because they are 100% equal with ${\textsf{\color{blue}/config/Mekanism.cfg}}$ "tier" and "usage".
The rest of the conflicts between ${\textsf{\color{blue}/config/Mekanism.cfg:}}$ and ${\textsf{\color{red}/config/mekanism/Mekanism.cfg}}$ can be easily resolved manually. (Personally I prefer the WinMerge tool)
Modpack 1.6.7
I found some possible duplications in the config folder. Everything works fine, just hard to overview and modify.
${\textsf{\color{blue}/config/Mekanism.cfg:}}$ tier{...} usage{...}
${\textsf{\color{red}/config/mekanism/Mekanism.cfg:}}$ -tier{...} -usage{...} tier{...} usage{...}
Currently the ${\textsf{\color{red}/config/mekanism/Mekanism.cfg}}$ "tier" and "usage" sections are ones the game is using.
${\textsf{\color{red}/config/mekanism/Mekanism.cfg}}$ "-tier" and "-usage" sections can be deleted, because they are 100% equal with ${\textsf{\color{blue}/config/Mekanism.cfg}}$ "tier" and "usage".
The rest of the conflicts between ${\textsf{\color{blue}/config/Mekanism.cfg:}}$ and ${\textsf{\color{red}/config/mekanism/Mekanism.cfg}}$ can be easily resolved manually. (Personally I prefer the WinMerge tool)