That depends on the answer to this question (I haven't played CC in years)
What is so special about the gate to the DBT in CC?
If my instincts are right and they usually...aren't - thats where Serge was killed/not killed right?
If thats the case (and I hope it is) pathways to the DBT appear where something that should not have happened, happened. Examples in this case are Serge living (blame Schala) and Lavos's defeat (blame Entity).
So I'm guessing (again) that the bucket takes Crono Team B to post 1999AD Lavos battle site for dimension A. The gate further back by Magus II marks Lavos's grave and the CT entrance to the DBT.
So:
1. New gate at EoT is just another dimensional vortex - sending them to dimension A (convenient)
2. Pathways to DBT appear at sites where time was changed by an external force.
maybe
