Comment 2 for bug 581241

It's not the way I see it. The idea is:
Before Pidgin:
|[V]|
- Set up chat
- Set up e-mail
- Set up broadcast

Pidgin installed:
|[V]|
- Set up chat (Pidgin)
- Set up chat (Empathy)
- Set up e-mail
- Set up broadcast

Pidgin installed and configured:
|[V]|
- Chat
- Set up e-mail
- Set up broadcast

Added Thunderbird:
|[V]|
- Chat
- Set up e-mail (Thunderbird)
- Set up e-mail (Evolution)
- Set up broadcast

Configured Thunderbird:
|[V]|
- Chat
- E-mail [Thunderbird shortcut]
- Set up broadcast

Configured Empathy (or any other app)

|[V]|
- Chat (Empathy)
- Chat (Pidgin)
- E-mail
- Set up broadcast

So you have the choice and don't have that annoying Set up chat thingy when your chat client (Pidgin) is set up already