As both routeNpingme and Aaron indicated, there isn't a practical upshot from a privileges perspective. Whether an account is added to the Site Collection Administrators group from the site collection provisioning area (in Central Admin) or from within the site collection admin options (in the site collection itself), the resultant permission and privilege set is the same.
There is a big difference worth noting, though, and that revolves around e-mail notifications. In previous SharePoint versions, the "Primary Site Collection Administrator" (as identified by SharePoint within Central Admin) was actually referred to as the "Primary Site Collection Owner." The current version of SharePoint no longer refers to the primary and secondary admins (from within central admin) as "owners," but I believe the underlying behavioral aspects remain the same.
Primary and secondary site collection owners are also site collection administrators, but they receive e-mail notifications pertaining to quotas, user access requests, automatic site deletions (if such behavior is enabled), etc.
For more information, this link: http://technet.microsoft.com/en-us/library/cc288243.aspx. The reference is for WSSv2, I know, but the behaviors are (again, I believe) the same. This is corroborated by the following links for WSSv3 and MOSS 2007 on Microsoft's Office site: http://office.microsoft.com/en-us/help/HA101577811033.aspx. Note how the "Manage unused Web sites" section at the end of the page specifically states that the site collection creator is the site collection owner, and that e-mail are sent to the owner and secondary contact.
I hope this helps!