While you lose out on some of the benefits in the short term, in the long term you get the benefit that previously hard-to-decompose monolithic legacy setups can be sliced and diced gradually until you have units that are reasonable to start rebuilding cleanly. This one of those areas where layers etc. really are quite useful.
E.g. lets say you have a web server with umpteen different web apps. Turn it into a single container to begin with. Then export and create an image out of the OS and web server, and dissect each of the web apps into layers on top and separate it into one container per app. Now test a clean base image and try to layer each app on top of it, and re-deploy individually as you've confirmed it works.