Another pic of big set of roots above the flare

What kind of tree is this? Is it grafted?

Ordinarily, any of the smaller roots that come out from the side of the trunk can and should be be snipped off. You have one there that is quite large and marginally above the flare, if it is growing outward, away from the trunk, it would be okay to leave. But if any part of it is turning sideways, around or back toward the trunk, they can become girdling roots as the trunk gets larger and the root does too.

Here is a link to a video on this subject. https://www.youtube.com/watch?v=fI12XNNqldA

note around 2:30 in the vid. :-)

This is an autumn blaze red maple. I ended up spreading the roots out as good as possible, and just barley covering with dirt up to that level.

Yours isn't the worse case that we've seen here and you might not have any trouble at all. You just don't want the main roots buried too deeply.

Those skinny adventitious roots are worthless to the tree and the tree won't miss them but they can become girdling roots growing aimlessly around the surface of the soil. So you might want to snip them.