We actually started building the app before Electron was released. They had just made the split to atom-shell and brightray.
Once Electron got it's footing, we migrated there. It's also easier for us to contribute upstream patches for things like touch events. (We launched swipe-to-archive a couple weeks ago.)
Atom is lagging behind Electron. It's still running on Electron v0.34.5 which was shipped in November of last year. They're trying to keep up, but the community of folks around Electron is growing fast.