When dock badges were first implemented, they were all enabled by default. Users (including myself) suddenly noticed that our systems were getting one hour of battery life and constantly running at ~20-40% CPU at ridiculous temperatures. @Harrumph made a great post with CPU stats to verify: GoldenChaos-BTT Support and Feedback Thread
The underlying code for dock badges hasn't changed since then. We were unable to find a true solution, all we could do is turn on as few dock badges as possible by default, which led to the current default setup of apple-only apps being enabled.
The holy grail, naturally, is being able to support enabling all dock badges at once by default, eliminating the need for user configuration.