Theoretically (maybe practically as well?) Bethesda is actively consulting with team ESO. My guess is that most original suggestions on lore and world design comes from Beth, then Zenio may or may not make some alteration to better fit their concepts.
This.
Remember also that this game takes places roughly 300 years before the start of the 3rd era, Arena took place in the year 399. Skyrim takes place 200 years into the 4th era, and the 3rd era lasted about 430 years (approx). So roughly 1000 years has passed since ESO would have taken place to when Skyrim has taken place. Unless Bethesda plans on going backwards, they do not have to account for much because they can simply say that so-and-so has since perished, been destroyed, has been all but forgotten, etc etc. Since the time of the ESO, we have seen the rise of Tiber Septim, the rise and now the apparent fall his Empire, and things destroyed that Beth has allowed the Elder Scrolls series to still have that slate from Skyrim to work off of.
I doubt anything an actual player, guild, or faction does in ESO will matter because we all learn eventually that the EP, AD, and DC all eventually become part of the Septim Empire, either by will or by force. We also know that most parts of that Empire have either broken away independently and/or forming their own Empire as well(Aldmeri Dominion). Maybe some of the Aldmeri Dominion lore will show up in ESO, but it is still going to have a basis in the told lore that we have already seen.
Also remember that Beth has already laid out how Tamriel is setup, where the cities are, etc. The only difference will be what Orsinium would look like since that has been sacked and rebuilt many times, and in various locations. Will things look different? I'm sure. There is up to 1,000 years difference for the landscape of Skyrim, 800 or so for the landscape of Cryodill, 770 for Morrowind, and at least 600 for the rest of Tamriel. The only one that might be close to it would be parts of High Rock and Hammerfell since parts of that province were in Daggerfall. The basic setup is already there though, but I think ZO will make a lot of decisions on detail and specific layouts, but they will do it under the general guidelines set forth by the lore of TES provided by Beth.