The Bug

In the noise settings, structures that generate in one dimension are defined.
In that definition, spacing, separation and salt is defined. Spacing and separation determine how structures are laid out.
The salt value is just an extra value that gets added to the seed. The seed + salt are used for the rng to determine at which coordinates the structure tries to generate.

Now, usually every structure has a unique salt value. That's important, since the structures otherwise would always try to generate ontop of one another.

Now, for bastions and fortresses, they are the same in the vanilla settings. That would be fine, if like it was initially, they didn't share any biomes. But now they do. Nether fortresses can now generate in every nether biome, and bastions can generate in every nether biome except basalt deltas.

This has the effect that for every location one structure tries to generate, the other will also try to generate, but only one of them will succeed, resulting in both generating much rarer because of it.

How to ... check

1. Download the vanilla worldgen files: https://github.com/slicedlime/examples/raw/master/vanilla_worldgen.zip
2. Check vanilla_worldgen/worldgen/noise_settings/nether.json for the salt values.
3. Check vanilla_worldgen/worldgen/biomes/... for verifying they can indeed generate in the same biome.