SharePoint permissions aren't confusing. Sorry I jest. They are pretty weak, but most of it comes because users ask for this granularity. Here's a 1 star rated excel document on SharePoint permissions, and it doesn't cover this core issue. Let me know if you find a better document on the detail around rights.

"I'm the owner of the site, the person who requested this site be created," starts a user as he describes his issue. I clarify, "Are you the site owner or site collection administrator?" He goes on to say, "Well, I have full control to the site." The discussion goes on, "Well, that still doesn't answer my question." Who is the site collection administrator? I'm not sure. From there we dive into his site and verify he is site owner and he does have full control. Then he goes onto the real issue. He's the site owner, and wants a new look and feel. Well, as site owner you don't have access to the galleries. Have you turned on the publishing features on your site? What? I can add the master page.

You can see there's a lot of confusion going on. First off, the Site owner is a very confusing role. It isn't described very well anywhere either. Essentially I see the best way to describe this role as the content owner. They are the NON technical owner of the site. The site collection administrator is really the person with the power. They are the one who can go in and activate the site collection features, not to be confused with the site features which if you try to activate publishing from there, you'll get a dependency error. If you want to have easy to use master page galleries and a nice drop down selector for managing your master pages and system master page, you first need the need the site collection feature activated. You'll notice that that managing the site collection features requires site collection admin rights.

When comparing the two, the site collection admin has "god" rights, but the site owner has "full control" from a content perspective within the site. It is better understood that file share equivalent may be thought to be full control as having full rights, but with SharePoint you're going to need site collection admin rights to better control the behavior of the site and to better manage the galleries of the site collection.

Below is a screenshot taken by Mike Smith who goes into the more intricate details of this issue in his post: Mike Smith's Training Notes on Site Collection Administrator vs. Site Owner (full control). Which compare the site collection admin rights (the full list) with those in red as NOT available to the Site Owner. The site admin vs. Site Collection Administrator is a similar set.

Microsoft's own documentation on Site Collection Admins describes the role:

"…As a site collection administrator, this means the following:

You might be expected to be the main point of contact between your part of the organization and your IT department.

You'll need to work closely with people in certain roles in IT, such as your SharePoint farm administrator.

You'll be performing some tasks that might previously have been referred to your organization's IT team, such as deciding who has access to important intellectual property stored on your organizations web sites (that is, setting site-collection level permissions), and deciding which features to make available to the people who will be using the sites in your site collection.

You'll probably be providing some technical support for the people who use your site collection."

If you decide you need to change the rights… Here are some simple steps:

1. At the top level of your site collection, click Site Actions and then Site Settings.

2. Under Users and Permissions, click Site Collection Administrators.

3. In the Site Collection Administrators field, type or browse to find the name of the person you want to designate a site collection administrator.

4. Click OK.

Summary:

The site owner is the content owner and has full control over content in a site.

The site collection admin controls the features, permissions, both content and technical management and has god rights across all content and galleries.