It's a pun on Wine, the syscall translation layer that lets you run Windows programs on Linux without hardware virtualization.

A working Wine configuration includes a directory that functions as a virtual C;\ drive, has a registry, and various other settings. You can actually have multiple of these if you specify which one to use at launch time through the environment variable WINEPREFIX, which points to a directory containing the relevant config files and other data directories.

A "bottle" is a user-friendly way of interacting with this functionality, managing these prefixes and their settings, and recommending known compatibility fixes for them. It may also involve managing multiple Wine versions, perhaps including some with patches.

It seems comparable to a lot of older tools in the same vein like CrossOver Linux (by Codeweavers, who maintain Wine), PlayOnLinux, Lutris (gaming-focused), and Cedega (gaming-focused and defunct).