Yeah, I thought that Sephiroth created a 'manifestation' of his will in order to release Jenova and do whatever else. This power is a result of Sephiroth's Jenova cells and the time he spent in the Lifestream.
The entity Cloud and co. encounter clearly uses Jenova's superhuman powers, yet it speaks in Sephiroth's words and from his perspective. Even though it's not Sephiroth's real body that the party chase, it still appears to be his mind in control (although we know that Sephiroth, too, was essentially Jenova's puppet, but that's just confusing the issue).

But whatever. I just like to think that it was actually Sephiroth, in one way or another, and not Jenova or some mindless experimental clone who I spent so many hours persuing.

*looks at topic: Two Sephiroths*

I believe that there was only one 'real' Sephiroth - the one in the North Crater. Besides him, there were his 'Illusory Sephiroth' and the men in black cloaks.

But hey, please don't read too much into my ideas. Any theory which fits the facts is just as likely to be right.