Atom isn’t designed to be network aware. All of its file access assumes local filesystem interaction. And I suspect that some of the optimizations that ExpanDrive uses kind of break the “drive” metaphor. For example, it states that it supports S3. One of the limitations of S3 is that if you write to a file and then read from that same file immediately, you may or may not get back what you just wrote. Whereas when you write to a local filesystem, if you read it back immediately, you are guaranteed that if the write is successful the read gives you back what you just wrote … even when things like caches are in the way.
With that said, there are systems that treat some kinds of network storage like really slow local storage with the same kinds of guarantees. I use sshfs all the time at work and Atom never runs into the issues that you describe.
Additionally, one of the eventual goals is to make Atom more network storage aware … but I don’t know of any planned timeline for that.