How to Make the Nether Roof and Floor Flat with Flat Bedrock
The Nether is the dimension where this mod changes the most, because it has bedrock both at the bottom of the world and at the top. By default the mod flattens both of those layers, so you get a clean, walkable surface instead of the usual jagged mess.
Confirm the Nether is being handled
Open the config folder at /config/flatbedrock/dimensions/ and look for nether.json. That file controls the Nether. It contains a dimension ID plus four true/false switches: genTop, genBottom, retroGenTop, and retroGenBottom. The gen switches control newly generated chunks, while the retro switches control chunks that already exist in your world. To flatten the roof, genTop must be true; to flatten the floor, genBottom must be true.
Flattening an existing world
If your Nether was created before you installed the mod, the gen switches alone will not fix it. Set retroGenTop and retroGenBottom to true so the mod reworks the bedrock in chunks you have already visited. Back up the world first, since retro-generation rewrites terrain. Once the values are saved, load the world and travel through the Nether so the affected chunks are processed.
Choosing the fill block
The fillBlock value decides what replaces the removed bedrock. Leaving it as the default stone-like block gives you a solid, buildable layer at the roof and floor, which is handy for farms and mob-proofing.