The farthest you can dig down is 8 meters from starting terrain level so no, you can't flatten every thing.

I wonder if creatures would also appear if you flatten the whole world under sea level. Currently I discovered an error in the mountains where a golem is reappearing every day though I kill him.

Mobs that appear randomly have specific spawn points. Wolves in the mountains spawn in specific spots. Greydwarves spawn in specific spots. Trolls spawn near troll caves or copper nodes. Golems spawn in specific spots usually near an abandoned mountain cabin or a silver vein.

Boars, deer, and birds also spawn in specific locations and once you find those spots deer and boars will respawn there every couple of in game days. Birds will respawn every couple in game hours.

There is also a bug in the spawn mechanic for deer and birds. If you have complete workbench coverage over a deer or bird spawn point they can occasionally spawn there anyway.
https://steamcommunity.com/sharedfiles/filedetails/?id=2860289081
https://steamcommunity.com/sharedfiles/filedetails/?id=2920176358
https://steamcommunity.com/sharedfiles/filedetails/?id=2924127097

berries respawn, berry bushes do NOT.
sticks and rocks etc that you can pick up spawn as well and can be difficult to remove at your base.
mushroom take a while to spawn and I recommend marking any spots with more than 3 so you can find if needed.

Mushrooms, dandelions, thistle, sticks, stones, and flint have stationary spawners that will respawn again after they are picked. Even if you build your house over a place where you picked one up, it will still spawn inside your house.

Bushes will respawn berries as long as you don't destroy the bushes.

Downed logs that are part of the landscape will respawn eventually.

Big rocks and ore nodes do not respawn.

Items that respawn mobs, like greydwarf nests and bone piles, will not come back when destroyed. Similarly, those boar runestones will not respawn boars.

For invisible spawners, some of them will cycle through appropriate mobs. If you kill off the boars, you might get necks there next time. And some of them spawn the same thing every time. Base items like workbenches and campfires will repress these spawns.

Most items inside dungeons do not respawn. The exceptions to this are yellow mushrooms, royal jelly and seekers in the mistlands.

I've noticed that with 'thistle' in the BF, the blue swirlies in the dark, seem to stop growing when I remove the trees nearby, as if they need the shade from the trees to grow?? Not entirely sure, but I may have destroyed them via combat. After an update, they seem to reappear in some spots where missing but not all...?

It can also be that you destroy some thistle plants when falling nearby trees.

They are not dependent on each other. You can cut down the complete forest and everything that was in there will still continue to respawn. Except for trees. You will have to replant them.
There is no special criteria for respawning of berries, mushrooms and other pickables. They will respawn on the same spot in several ingame days. I think the most of spawners have 2-4 hours respawning time.

ah gotcha, tyty