Yes, it did happen at the soil line!

Can I put the area below the soil line again or should I keep it risen up like this? And how can I avoid this type of damage on the future? (I also have a few Adeniums.)

You can keep it above or you can plant it back down and it should be fine. If it happened a while ago it has likely already healed and the scar will eventually fade over time. But, keep your gravel very slightly pulled back so it doesn't have direct contact with the skin of the tree if it is exposed to full sun. Or use a much smaller, finer gravel, or a fine pine bark, or if your conditions allow, live moss is nice (more ideal in shaded trees).

I wanted to bury it but I was afraid to cause rot. I'll definitely pay better attention to the gravel around the soil line.

If it just happened, I would keep an eye on it for a while to be sure it's nice and dry, and isn't soft or spreading. I assume your temps are not hot and sunny this time of the year so if it happened recently, it may not be a burn like I suggested. If it happened last summer though it likely was.

If it's months old, firm and dry if you press on it, you should be fine to set it back down. Be sure the mix you add is nice and gritty with lots of air so what are now the surface roots don't stay too wet and are given time to adapt to the greater depth.

It is at least that old. It is firm and hard/dry. It has been since I discovered it. I'll also get a deeper pot for it when I lower it, that should help the surface roots stay in a more similar condition/water level.

I'm glad I don't have to cut it out. If it were your plant, would you lower it or allow it to just be ugly above ground until it grows out of the scar?

No, don't cut it out. That would scar it much worse and add the risk of rot. There's no reason to cut it out as it is no threat to your plant's survival as it stands now. It would only do more damage. If you really couldn't stand looking at it, you could cut or air layer your plant right above the scar and try to root it anew, but again there's more risk in that than necessary.

And really, there is no need. Yes, once I get a plant with such a scar caused in this manner, I simply put it down slightly lower to cover it up. Also, at least on an adenium, those parts we bury in the substrate actually grow faster than if they are exposed. So it would speed up the process of filling in the dent and smoothing away the scar. I am less familiar with your specific plant type.

Now if this scar was not smooth, and was craggy and might trap moisture, bugs, etc that was inclined to lead to rot, then I probably wouldn't bury it. Certainly not without doing certain other things to it first. None of that is necessary in this case.

It does have a pruny appearance inside the scar. The raised areas are the vertical red/brown/orange stripes and the sunken areas are the white parts.

I think it'll be fine.