User blog comment:Commdor/What's Next for Mass Effect 3?/@comment-5503561-20120723015039/@comment-4721065-20120723101531

Actually, Atlas is a unique Cerberus design, something that no-one else possesses. As such, I think that it a good ol' Atlas that has been captured via killing the pilot and thus had to have its cockpit replaced with an inferior Alliance/asari/salarian one (the wiki page specifically says that the Cerberus cockpit material is a technological breakthrough in and of itself, and no-one is even sure about its exact composition). The warning stripes and different coloration are thus nothing more but a simple paint job.