A simple class to check if a Chunk is the start of a Fortress or not. For Spigot and Minecraft version 1.16.4.

Test_v1_16_R3.java

/*
 * MIT License
 *
 * Copyright (c) 2020 Marvin (DerFrZocker)
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in all
 * copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 * SOFTWARE.
 */
package de.derfrzocker.testplugin.fortress;

import net.minecraft.server.v1_16_R3.*;
import org.bukkit.craftbukkit.v1_16_R3.CraftServer;
import org.bukkit.plugin.Plugin;

import java.lang.reflect.Field;
import java.util.Objects;
import java.util.Properties;
import java.util.Random;

public class Test_v1_16_R3 implements Runnable {
    private final static int LENGTH = 2000; // in chunks
    private final static Random RANDOM = new Random(78923459872345L);
    
    private final DedicatedServer server;

    public Test_v1_16_R3(Plugin plugin) {
        server = ((CraftServer) plugin.getServer()).getServer();
    }

    @Override
    public void run() {
        StructureManager structureManager = new StructureManager(null, null) {
            @Override
            public World getWorld() {
                return null;
            }
        };

        long seed = RANDOM.nextLong();
        ChunkGenerator chunkGenerator = createChunkGenerator(seed, WorldDimension.THE_NETHER);

        for (int z = 0; z < LENGTH; z++) {
            for (int x = 0; x < LENGTH; x++) {
                ChunkCoordIntPair pos = new ChunkCoordIntPair(x, z);
                ProtoChunk protoChunk = new ProtoChunk(pos, ChunkConverter.a);

                chunkGenerator.createStructures(server.getCustomRegistry(), structureManager, protoChunk, server.getDefinedStructureManager(), seed);

                StructureStart<?> structureStart = protoChunk.a(StructureGenerator.FORTRESS);
                if (structureStart != StructureStart.a && structureStart != null) {
                    // The chunk has the fortress as structure
                } else {
                    // The chunk has not the fortress as structure
                }

            }
        }
    }

    public ChunkGenerator createChunkGenerator(long seed, ResourceKey<WorldDimension> actualDimension) {
        Properties properties = new Properties();
        properties.put("level-seed", Objects.toString(seed));
        properties.put("generate-structures", Objects.toString(true));
        properties.put("level-type", "default");
        GeneratorSettings generatorsettings = GeneratorSettings.a(server.getCustomRegistry(), properties);

        RegistryMaterials<WorldDimension> registrymaterials = generatorsettings.d();
        WorldDimension worlddimension = registrymaterials.a(actualDimension);
        ChunkGenerator chunkgenerator;
        if (worlddimension == null) {
            chunkgenerator = GeneratorSettings.a(server.getCustomRegistry().b(IRegistry.ay), server.getCustomRegistry().b(IRegistry.ar), (new Random()).nextLong());
        } else {
            chunkgenerator = worlddimension.c();
        }

        try {
            Field field = ChunkGenerator.class.getDeclaredField("injected");
            field.setAccessible(true);
            field.set(chunkgenerator, true);
        } catch (NoSuchFieldException | IllegalAccessException e) {
            e.printStackTrace();
        }

        return chunkgenerator;
    }

}