After lots of research for issuing mergetool with vimdiff and only 3 windows, I came up with this configuration, that allows me to chose when I want 3 windows or the default 4 windows:
git config --global merge.tool vimdiff
git config --global alias.mt mergetool
git config --global mergetool.merge3.cmd 'vim -d -c "wincmd l" "$LOCAL" "$MERGED" "$REMOTE"'
git config --global alias.m3 'mergetool -t merge3'
Now you can start 3 windows just typing:
git m3
And the default (4 windows) will still works as expected with:
git mt
Also, you probably would like to add this lines to the end of your ~/.vimrc or /etc/vim/vimrc
 " shortcuts to vimdiff
 let mapleader=','
 let g:mapleader=','
 if &diff
    map <leader>1 :diffget LOCAL<CR>
    map <leader>2 :diffget BASE<CR>
    map <leader>3 :diffget REMOTE<CR>
 endif
This will create shortcuts like ,1 to grab from left, ,3 to grab from right (in both modes) and also ,2 to grab from base (center window) in the 4 windows mode.
That helps a lot!
My ~/.gitconfig file looks like this:
[user]
        name = Dr Beco
        email = my@email
[merge]
        tool = vimdiff
[mergetool "merge3"]
        cmd = vim -d -c \"wincmd l\" \"$LOCAL\" \"$MERGED\" \"$REMOTE\"
[alias]
        lo = log --pretty=format:\"%h %ce %cd %s\" --graph
        co = checkout
        ci = commit
        cm = commit -a -m
        st = status
        br = branch
        m3 = mergetool -t merge3
        mt = mergetool
[diff]
        tool = vimdiff
I hope this helps you (and those who get to here).