It actually is encouraging people to have useful user agents. By default most people end up with a user agent that's something like "libcurl version foo.bar.baz", which isn't actually a description of who or what they are; given the prevalence of curl, it really just tells you that it's a program that uses http.
They did not. Automod was created by a user as just another script that interacted with reddit's api (albeit, a powerful and useful one). Deimorz eventually joined reddit and became an admin, and Automod was eventually integrated into the site code (primarily for performance reasons), but that was completely user-created, and in fact a great example of how reddit's community governed the site for a long time in absence of much direction from reddit Inc.
Okay, user created, and promoted to be on-server and faster by reddit. Automod is a heavy-handed tool that both mods and admins played a role in creating.
> The problems Reddit is facing now are largely a result of the admins getting more activist as Reddit is more visible than ever.
Really? It seems to me that the problems come from not banning things, still: see all the complaints about racism and other "undesirable content" on the site.
They're just like other default subreddits, which is to say that you can unsubscribe from them. I only resubscribed recently because I started working at reddit and figured I should know what's going on in my own company.