I don't think "huge projects" factors into it at all, no reasonable source file should ever come anywhere close to the Atom file size limit. If you have 13MB source files you have more serious problems than your choice of text editor.

The kind of files that choke Atom are large data files that there are usually better/different tools for, that have very different requirements from code editing. And that has little to do with the relative huge-ness of your projects.