The Epoch certainly does seem to have sentient qualities. However I believe the fact it travels time differently than the gates (thus bypassing the Conservation of Time). Not only that, three people are traveling within it. Now, we can argue that a pregnant woman might cause some chaos in the space-time continuum, but I believe the fact that it is within the being, that it still counts as part of that being. Using the Epoch (if the Conservation of Time still applies to it, if it creates its own temporary gates) means only one entity is traveling through time.
Another question, Magus' gate. Four people entered, yet they were cast into different time periods, rather than ending up at the End of Time. This may be Lavos' influence, and the fact that Magus remained in the center while Crono & co. were spun around, and being such a large gate, the center (Magus) went one place, while the orbiting party was cast elsewhere. Thoughts?