If you can get to it, you might try a nut splitter, you can get them at most automotive and hardware stores, it slips over the nut to the side, and has a screw in the end that drives a cutter into the nut which splits the nut, allowing it to be removed. This is probably brass so it should be easy. Otherwise, try a few standard things first, penetrating oil or WD-40 and leaving it overnight, then, last of all, vicegrips on the bolt if you can reach it, true, the top threads will be damaged but you can probably cut the bolt under the nut at that point, you'd be best to replace the bolts when you get it apart. Another method would be to carefully drill into the bolt itself, from the top, and insert an "easy out" which is a reverse threaded tapered screw, usually designed to extract a broken bolt, but in this case, it will stop the screw from turning while you undo the nut. Try the simpler fixes first. If you have to cut something off, dremel-type tools are great for that, much more compact than a full sized angle grinder. Wear safety glasses or a face shield all the same.

The flange is supposed to rest on the finished floor (but not higher). If it's up in the air, that's another story and would have to be fixed. Your toilet could be wobbling because the floor isn't level. If so, plastic shims from the hardware store will help.

Good picture! Ideally that is what you'd have, the flange sitting on top of the floor. With new construction or a plumbing repair, that is the flange elevation that the plumber should shoot for. If a leak occurred between the toilet and the flange, fluids would remain on the non-porous tile. In a remodel if the flange is a bit higher than the floor, that can work, but if too high the bottom of the toilet can come close to, or even bottom out on the flange. That leaves inadequate to no room for the wax ring to create a proper seal. A broken seal can lead to sewer gasses, or when you plunge or the toilet is flushed, a leak. Too high of a flange can even lead to a rocking toilet. You don't want the weight of the toilet bearing directly on the flange. If the flange is below the surface of the tile, that can lead to issues as well. First and foremost, too much space between the bottom of the toilet and the flange. That can lead to the wax ring not properly filling the gap. Odors, leaks, etc. Some folks will double up with two stacked wax rings or use an extra-thick ring, but they can displace when the toilet is set. If there is a leak with this setup, fluids can end up directly on the subfloor. Repeated wetting leading to water damage could be an issue. And why not add more? Look at waxless boot-type toilet seals, like the Fernco Wax Free seal. You need to replace a wax ring whenever the toilet is pulled. With the Fernco, you generally buy one and it's good for the life of the toilet. Enough toilet talk. Time to go outside and work on my wood-fired pizza oven!

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