This is a "it depends" type of question.
The rule of thumb is, if the user typically sees information in both sections as being closely related and will commonly edits both sections at once, then yes it make sense to have everything editable at the same time. If however, the two sections are distinctive enough that when a user is editing one section, they might not necessarily need to deal with information in the other section, then it'll reduce their cognitive load if the other section isn't a part of the form.
In the case of editing user info vs permissions, it seems like the latter case is true. As an admin, I need to update the user's contact info. I might not necessarily need to update that user's permissions. In fact I'd guess that it's pretty rare to need to do both at once. So why present more fields for the user to deal with using a giant form?
Onto the "Create user" scenario. As an admin, when I create a new user, I probably want to put in the name and contact info for the person, AND I'll need to configure their permissions. There's no case in which the admin wants to add a user into the system and not set up permissions (unless the system has a default set and majority of user use the default, even then I'd probably also want to glance at them to confirm everything is ok).
So we can see the "Create" scenario follows the first case. Which mean it makes sense to put it all together in.
And it's okay that "Create" process is different than the "Edit" process, because the use cases are very different.