In System Preferences > Notifications, there are two entries for Google Chrome, and they have different settings.
I can obviously change them both to what I want, but why is this happening and how can I get rid of the extra one?
The new answer
The reason why you see two notification sections in System preferences is because one is for calendar (That is the one with the banner) and one regular notifications (the one that controls website notifications
The old answer The reason why this answer is not right in your cause is because this is for Chrome's settings
If you have multiple accounts on your Google Chrome browser, you can change the notifications for both accounts. If you want to get rid of a Google Chrome notification panel, simply get rid of the account that you are not using anymore. The reason why they have different settings is that the primary account will show up different then your other accounts.