Making Git retain different section content between branches

All your changes should be merged except changes to those values, which makes them not like the others, not changes to intrinsic content but deployment-specific changes. Those might be best applied in the post-checkout hook. Here’s a sample, a per-branch include processor

cat <<\EOF >.git/hooks/post-checkout
#!/bin/sh
if branch=`git symbolic-ref HEAD --short -q`; then
    for file in `git ls-files -cix*.@branch`; do
        echo "* making ${file%.@branch} from $file with branch-specific includes"
        echo '/^@include-branch-specific ([a-z/]*)$/ { s//cat \1.'$branch'/e }' \
        | sed -rf- $file >${file%.@branch}
    done
fi
EOF
chmod +x .git/hooks/post-checkout

# testing
git checkout beta

cat  <<\EOF >config.@branch
// ==UserScript==
@include-branch-specific config
// ==/UserScript==
EOF

echo >config.stable '// @downloadURL  --  StableURL File Location'
echo >config.beta   '// @downloadURL  --  BetaURL File Location'

git add config.*
# git rm --cached config
git commit -m'setting up per-branch configs'
git checkout

git checkout stable
git cherry-pick beta
git checkout