I think its a good idea to merge the unbundled watcher (excluding the server and tray) into official ActivityWatch as a submodule named aw-watcher-linux. The Makefile can then be updated to build this watcher instead of aw-watcher-afk and aw-watcher-window if the platform is Linux. This would allow ActivityWatch to work out of the box for Linux users without requiring manual installation.
If possible, could you create a branch without the server and tray? That would be a great help. Let me know if you have time to look into this.