I looked into DotEnv.jl, I think I avoided it because the package hasn’t been updated in so long I thought maybe it had been abandoned/wasn’t supported anymore 
Is the persistence across projects the only downside in your view? In the very specific use-case I’m thinking of that sparked this question (an internal analytics package), a limited set of variables shared amongst all projects is not necessarily a bad thing! For example, if you’re only using one database for all your projects then it makes sense for those credentials to be accessible across projects.
But I can see how this could get messy if credentials were highly project-specific. In which case .env files would definitely be the best way to go as far as I can tell.