Atlas is electronically Lionel inside, so they will run as well as any Lionel locomotive having equivalent levels of electronic features. The early Atlas had no cruise control, but run pretty well. Legacy should run Atlas as well as it runs non-Legacy Lionel/Weaver/K-Line TMCC - I have the "reverse" experience with that - I have TMCC on my layout, but I do have a couple or three Legacy locos (SD-40-2; USRA 2-6-6-2, for example) and they run just fine under TMCC - as they were designed to do.
The same should be true of Legacy/Atlas, I would think.