Huh, that text is quite interesting... I never saw it, though. o.O All I saw were the originals saying the "ZOMG r u me?!?!?!?!" lines. The clones just immediately went into a fighting stance after that, and the battle started. It must be some unused/dummied text. Odd. I also found it strange that the Steel Shade battle was the only one the party reacted to. (I loved Janus's line though. :p Went something like, "Whether you are the real Crono or not, I will not hesitate to destroy you!")
And yes, it does seem like the shades have some connection to the ghost children in CC... Perhaps the children at the Dead Sea and the ones in Terra Tower and on the beach are actually different entities? I know this has been said before, but the Dead Sea children are much angrier and hateful towards Serge, whereas the Terra Tower ones are just like "Hey, you have the Chrono Cross. Cool. How's life treating you?"
Also, we can't really be sure about what happens in the "Ideal" timeline at the end of Cross. We're just shown one small scene, and that's it... We have no clue if Guardia's now suddenly...not fallen, or anything else, really. o.O
Gah, it's so confusing! >.< Hurry up Ultimania, we need that guide fast!