That is the most unexplained answer. Simply saying that it's TTI or that Time Bastard does not work in this matter is BS.
As for Terra Tower - It was to far away from Chronopolis.
Lavos could not be stopped when he destroyed Zeal because of this. He left his PD destroyed Zeal then created a new one probably. That or because we don't have a chance to destroy him before 12,000BC because nothing allows you too. The destruction of Zeal comes to pass, and nothing can make you go back to before that, probably the real entity's doing cuz it doesn't want Zeal or something. The major point was only to destroy him from 12,000BC before 1999AD. Basically, anything prior to 12,000BC cannot be changed. Anything after the Ocean Palace disaster can be.