Following scenario: One Crowd server, three JIRA servers connected to it and six Confluence instances. If you are an administrator on ANY of those connected applications, it would appear that you can a) add new users to Crowd and b) add them to groups that have NOTHING to do with the application that you are an administrator for.
Yes, so long as the default directory they are creating a user in is connected to all of those instances. All groups are pulled in directly from Crowd across all instances because they don't know what's restricted to them.
If you'd like to limit this, you could add a new directory. Additionally, you should be able to limit the LDAP filter for each instance it touches to help refine as well: https://confluence.atlassian.com/display/CROWD/Restricting+LDAP+Scope+for+User+and+Group+Search
Essentially what Crowd-administrator does is lets you modify/access the Crowd Administration console directly. I can see why you would feel like its sort of backwards, but the way that the Crowd directories work is that if you connect it to JIRA or Confluence, and you are a in the jira-administrator role, you should be able to create the same way as you would have. It all depends on the directory configuration.
There are ways to break this, which you can search for, but I wouldn't suggest it if you're trying to lock it down that way.
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