Let's delve into some alternate history speculation. Lets say that in an alternate timeline, the Heart of Lorkhan was never discovered by the Dwemer. Many of the most important events in the history of Tamriel would not have happened. Here is a list of the consequences I can think of. There are probably many more.

• The Dwemer didn't disappear.
• The Dwemer and the Chimer could've remained allies, since the Battle of Red Mountain was caused by the Chimer getting angry at the Dwemer for creating their false god.
• The Tribunal didn't come to power. Nerevar and Voryn Dagoth most likely stayed alive.
• The Chimer were never cursed into the Dunmer.
• House Dagoth wasn't destroyed.
• Without the controversy over Nerevar's death and the strife between traditionalist Daedra worshippers and the Tribunal Temple, the Ashlanders wouldn't be so opposed to Great House society.
• Lie Rock wasn't stopped by Vivec, and the disaster it caused would've came much earlier.
• Without the Tribunal defending Morrowind, the Reman Empire would likely be more successful in their invasion.
• The Kamal Invasion wouldn't be as easily repelled due to the absence of the Tribunal.
• Tiber Septim didn't conquer Tamriel with Numidium. As such, Wulfharth was never betrayed and Zurin Arctus remained alive.
• Much of the events of Daggerfall and Morrowind would not have happened.

What would happen in a Tamriel with these differences?

It would be a different series. Everything would be unrecognizable.

And Cyrodiil would still be a jungle

They eventually probably would have been wiped out by the Nords, Chimer and revolting Betrayed unless they fled deeper underground, the Dwemer in Hammerfell and High Rock would probably survive. Then likely most of the points you listed.

Would Sheogorath have even bothered to toss that rock at Vvardenfell?

Good point, there. Though for all we know he would've decided to throw the rock at the Imperial City instead.