You've gone deep enough on tree 3!
On tree 3 I would say use a couple of inches of compost to layer into that hole and leave that saucer shape in place. You may be down a couple of inches deeper than you need to be, so the compost will give the hole a nicer look, conceal some of those lower roots, and will give the tree a nutritional boost. Don't fill the hole or plant flowers or anything in it and you might want to bevel the hole out a little farther all around to give it a saucer look.
On the 2 sets of photos of tree 1 that has a girdling root (the roots that make a tight wrap around the base of the tree) you would probably do more harm that good to try to pull it off or completely away from the entire trunk, but if you carefully sever the root just beyond the twist on the bole where it a cut won't hit the trunk, then the tree will continue to grow and will absorb and surround that now-cut-off old root. If the root continued to grow it would grow against the existing trunk and girdle or strangle it. It looks like the flare isn't completely exposed yet, but you can do this in baby steps.
I've saved and marked points where you should sever the girdling root on the roots you see now. I suspect that those are all adventitious roots, the kind that sprout from the bole into the surrounding soil, but aren't true roots and the tree doesn't need. It looks like you could probably trim off all of those wrapped roots.
For the time being, I think I would leave tree 3 exposed like that (you may want to shape that saucer outward a bit to give it a nicer look, that's just a personal choice) and use a fine layer of mulch to cover the exposed dirt. Maybe 1/2 inch, just to cover the soil. See if the tree improves over the next few months. If you remove the adventitious roots and can poke carefully around in the bottom of the hole to find the trunk flare then you might remove a little more.
I'm not a arborist, I'm another organic gardener who has dug out a few of her own trees that were too deep in the ground. I have a bald cypress out back that resembles your tree 3 - I probably need to cut off adventitious roots and dig a little deeper to expose the flare. I've left it as is for a time to see how it responds, and I think after a couple of years exposed like your tree it hasn't responded as well as I'd hoped - so I'll probably take time this fall and remove the adventitious roots and go a little deeper. If I end up killing this tree, it would be sad, but it hasn't grown the way it should (in 13 years it should be huge by now) - if I replant a new tree the way I know it needs to be planted I'll catch up to the size of the current tree in a year or two. Yes, planting them too deep in the ground really does stunt the growth dramatically.
Tree 1b-marked.jpg [ 466.68 KiB | Viewed 134 times ]