"he point is going forward Atlas would be better off with a single command system used my dozens of manufacturers"
Maybe, maybe not. I'm sure Lionel (and Atlas) are doing the math as to whether it would be better to include another command system in their locos. If it becomes desirable due to inability to keep up with technology, or cost or related issues, I'm sure they'll do it.
Right now, the vast majority of three railers use TMCC/Legacy, DCS or conventional only, or some combination. Addition of DCC might only increase their market by tiny amounts. Two railers are a different story, of course. DCC is the only thing that makes sense for command, although most two-railers probably still use conventional. Broadway Limited just reverted to offering locos with DC and no DCC/sounds as it saves these people $100-150 per loco in HO and N.
Atlas knows that their locos have to be operable by the majority of hobbyists, who still have Lionel based systems, either conventional or TMCC/Legacy and I'm sure that will figure into their choices going forward. Currently they are offering both PS3 and TMCC equipped three rail locos. At some point they may well decide to go with only one of those systems, and PS3 might make sense as they can include DCC for the two railers.