Hello byaccident, I know what you are talking about with winmerge, I am gonna tell you my setting in winmerge maybe it will help you. You will still see alot of yellow but not whole different files.
One thing that causes that is dotnet 4 things they introduced into servuo.
Ok here we go, open winmerge then under edit then options, under options then compare then general. make white space = ignore all. then under that check ignore blank lines, ignore case, ignore carriage return differences and match similar lines. Hope that helps you out some, it sure helped my merges so every file wasn't all yellow.