On EndeavourOS forum I saw this cool helper implementation of running meld as root
#!/usr/bin/bash
set -euo pipefail
export PATH=/usr/bin:/usr/sbin
for i in $(/usr/bin/pacdiff --output); do
echo "Merging $i ..."
/usr/bin/meld "admin://$i" "admin://${i/.pacnew/}";
done