Just want to seek clarification on how checkout should be used. As the way it is now, some are using it for payment while others are using it in a version control context. If there are more appropriate tags that should be used for either scenarios, feel free to suggest those as well.
Well, at the risk of sounding obvious, you could just leave it the way it is.
It's highly likely that questions having to do with version control will also have a tag that ties it to version control, like git or svn. You can find all of the git checkout questions using this search, for example.
Similarly, those questions that have to do with web development will have tags like magento, google and paypal In fact, this search, which excludes all of the major source control systems, will get most of those.
I don't think we need to change the tag at all. The concept is already so specific that separating them into different types of "checkout" will just make them too localized. and you'll have to ban checkout to keep people from using it (it's a naturally-occurring tag).