All colors are configurable through Visual Studio Tools / Options menu then Environment / Fonts and Colors and finally search for Git Diff Margin Addition / Modification / Removed

In your .gitconfig for the repository or for your user you must have a [diff] with tool = and in the [difftool] a .exe, $LOCAL and $REMOTE

Example for Semantic Merge tool

[diff] tool = semanticdiff

[difftool "semanticdiff"] cmd = C:/Users/Laurent/AppData/Local/PlasticSCM4/semanticmerge/semanticmergetool.exe -s "$LOCAL" -d "$REMOTE"

[difftool] prompt = false