If there is a space after a line in server.properties the line gets ignored and doesn't seem to throw any warnings (at least none I noticed).

he specific issue I was having was with a mod that creates flying vehicles, allow-flight=true was set but was ignored because it had a space after it (which took me forever to figure out). Minecraft should ignore or even correct such spaces (from my limited experience it should be rather easy to add a check for it).