So its an UX issue for you, because it doesn't embbed in the Synology ui. True, I can see where you come from.
So if no package is available and you would need to install and configure an application (take any php webapp) you still want to run on your Syno is less messy and easier to accomplish then setting up a docker container? Can't agree on that. On the contrary: someone put in the effort to automate the installation and configuration and provides variables to configure the relevant configuration aspects. While on a self installation and configuration you are by your own with every single aspect.
The comparision with WinAmp is kind of funny, though is a complete different caliber. A docker container is a ressource saving way to run a process on the host that "thinks" that its on it's own machine. The overhead is close to nothing. Docker is not intended for GUI applications - every container wrapping a GUI application is always ugly. Docker is more suited for apps/services that preset a web-ui or a service to connect to.
Docker is simply a way to bypass limitations of the appliance stlye DSM OS, without messing arround with the base os itself. At the end it's a matter of taste.
Update: fixed some typos