The Time Kompressor herself has reason to be confident going into this match. Good reason. Her opponent is severely outmatched in the HP department, being only a PC compared to Ultimecia's obscene-even-by-final-boss-standards level HP. As well, Ultimecia has much more variety in her repertoire than the boy from Arni. Her Apocalypse spell is deadly as ever, and other attacks will serve her just as well. In fact, given her HP, their high power doesn't even matter, since she could just wear him away with them over time.
V
S
From Chrono Cross.
RC Serge can cross dimensions. Hooray for Serge.
Ultimecia can kompress time. Hooray for Ultimecia.
Logically, it would seem that these two are evenly matched.
That would be assuming that one didn't look at anything other than plot power. And, like in most cases, a good PC cannot beat up a decent endgame boss. Thus, Ultimecia dances on Serge's grave. Well, where his prone body was before it was absorbed into the timestream.