I worded that poorly - a sprite atlas offers no performance advantage at all with FlashPunk. The only thing that makes a difference is whether you are using transformations or not!
However, if you were to hack FlashPunk to use GPU mode properly, a sprite atlas might offer a small performance boost on mobile… But it’s probably more work than it’s worth!
As @rostok pointed out, depending on your game you might save a bit of memory using it… but I don’t know if that’s worth the effort unless you’re using huge sheets of sprites. Oftentimes your development time will be way more important than any memory usage gain - you could use that time to improve your gameplay mechanics or game art for example, rather than spending it doing optimisations that might not actually make any difference at all for 99.8% of the people playing your game.
Premature optimisation is bad juju.
When the time comes that you might want to put the game out on mobile I have a solution if you don’t mind publishing with us on certain platforms. More details later as I’m planning a release this week, but long story short my Stage3DPunk engine handles rendering with Stage3D as well as automatically assembling these sprite atlases at runtime (albeit not very efficiently, but enough to give a decent performance boost in Stage3D mode which very much relies on sprites sharing textures).