My belief is that there is only one Tesseract for every timeline/dimension. It is said that discarded timelines go there. Certain timelines persist for a purpose, most likely at the behest of the Entity. The only other possibility for Dinopolis' introduction into the world is that the planet can pull stuff right out of the Tesseract. A timeline is the exact same thing as a dimension, technically. Every alternate dimension is another timeline, another way the universe could have developed. Therefore, the Time Devourer is a unique phenomenon to the Keystone dimension, but due to its heightened ability to facilitate time and dimensional travel, it poses a threat to the entire omniverse. The only dimension actually fated to exist is the Keystone dimension -- all others are floating around in the Tesseract somewhere. However, as I've said, certain phenomena could possibly allow timelines which would normally go into the DBT to persist. The Entity would be one such thing, whether it is indeed the planet or not.
As for civilization today and it being almost on par with Lavos, I'd have to take issue with that. Lavos survived a multi-gigaton impact into Earth 65 million years ago. We possess no weapons of anywhere near that caliber. In fact, no weapon we have ever tested, to my knowledge, has exceeded a yield of 100 megatons. Only the technology of Zeal could have dealt with him. Lavos must have realized this, because he destroyed it. But, he let the Black Omen/Ocean Palace live as a gigantic shrine to his power and a way to summon him out of his time bubble. However, some of the technology of 2300 AD resembles that of Zeal.
The Flame, seeing as how it splintered off in the crash, does seem to be a part of Lavos directly involved with thinking, or at least made so by him. In fact, given that Lavos inhabited a time bubble opening into the Earth's core, rather than the core itself, the Flame would be his only avatar in the world, because in CT he inhabits a time bubble, and in CC he's stuck in the Tesseract.
As for the Time Devourer evolving in the first place, he started the mutation right after the fall of Zeal. However, on that timeline, since neither El Nido nor the Dragons existed, he could not facilitate his full mutation. Therefore, one possibility is that he simply allowed himself to be killed in the time bubble and put up little more than a token fight against Crono and friends. This seems to massacre the point of the original CT, not something that I particularly like. However, there exists another possibility about why Lavos couldn't put up a full fight against either of his major opponents. I shall delve into that in a bit.
In this way, Lavos would be using Crono to create the new timeline, on which Chronopolis existed and could be pulled back in time. This would piss off the planet, who would then violate the laws of time to get Dinopolis into Keystone. Of course, Chronopolis would win the fight, allowing Lavos to absorb the Dragon God's full power right after it created Harle and got split into six. Lavos created the Dragon God avatar in order to manipulate Serge into allowing him access to the lost Frozen Flame. Perhaps Lavos was still able to use the Flame after it left him, but it would only regain its (and his) full capacity when it returned to him. THIS is the reason why Lavos couldn't use his full strength against Crono -- the lack of the Frozen Flame. Humans getting their hands on it served as a double-edged sword for Lavos -- it would enable him to get the best possible genes and energy out of this planet to pass on to the next generation of Lavoids, but it would also create opponents that could destroy him. I guess it was a risk he was willing to take -- there were risks involved in landing here in the first place, after all.