no messy system or leftovers. some programs use directories all over the place and it gets annoying fast if you host many services. sometimes you will have some issue that requires you to do quite a bit of hunting and redoing things.
docker makes this painless. you can deploy and redeploy stuff easily and quickly, without a mess. updates are painless and quick too, with everything neatly self-contained.
much easier to maintain once you get the hang of things.