A lot of non-vanilla system in disco or those heavily modified have errors and missing properties for various objects. Technical quality has never been a particularly strong point of mod's content, rather the opposite. Ain't helped by plenty of bugs in Freelancer rendering. When encountering these inexplicable bugs what I did was to have an empty isolated test system, place the content affected there or better yet recreate it and test if the issue persists. For your particular case I'd have exclusion zone within nebula and have those large asteroids within it while ensuring their bounding box does not extend into the border of exclusion zone.
After all in old Omicron Iota I had those large base structures within the nebula and I hadn't any visual glitch that would show them from outside, same goes for Ravine base in 99 (or whatever it is called nowadays) and it's about the smallest nebula+exclusion with base inside I could do without having pop-up glitches.
Nope, the exclusion zone didn't change it. It's big enough and has practically the same values like the exclusion zones used in the original nebula.
The same didn't work in my new system as well - it's isolated, is practically just a copy of the down-to-zero reduced Londonderry system, has a sun and somewhere else a nebula with exclusion zone that doesn't even visualize the jump hole. It's targetable though.
Could the issue be caused by the Freelancer Mod Studio? I literally tested everything you told me so far, most of it twice, but none of it seems to work. Could you maybe make a simple tutorial video that shows how you place a nebula with a rock inside that works? I mean, I must have done something wrong, but basically I have everything done I was supposed to do. The nebula.ini is there with all the values that are neccessary, as I took previous existing nebula for example. I have the system.ini, I have the zones and the exclusionzones. The nebula is big enough - even making it bigger than the original nebula didn't work - and the exclusion zone didn't help here either. Aside from that, the rocks in the Omicron Delta Edge Nebula are not part of an exclusion zone.
Sadly, Vipex didn't make that part in his tutorial. Placing asteroid fields works perfect.