Is it always necessary to run etckeeper git commands using the vcs command?

I've seen some tutorials on the internet in which people are using etckeeper to keep a log of their server configuration, and yet they use the git command directly instead of running it through the etckeeper vcs command. This seems a little dangerous to me, since etckeeper is a proxy for the git command since etckeeper has to store file permissions and meta data in the .etckeeper directory . Is running git commands like this dangerous to the state of the .etckeeper directory or anything else related to it? Does it depend on which command is run? Why or why not?