Better mineshafts makes them spawn in the aether aswell... which looks kinda cool but breaks immersion. So either a config entry like you have for the bridges. or just straight up disable spawning in the_aether:the_aether. :)

Past versions of Minecraft handled structure spawning in very non-user-friendly ways. I no longer support pre-1.18 and as such this won't be fixed, but dimension stuff can be fully customized to fix your problem in newer versions (1.18+) via data pack