Can you prevent the generation of resources that do not normally appear on nauvis? (or remove them on generation)
https://i.imgur.com/YQLrZRp.png

I think it's possible, but I'm not sure how. I don't quite remember how this mod gets surface settings, but I would guess it copies them from Nauvis. Not sure how Space Exploration handles resource generation on different surfaces, but I can tell you it's tricky to make different world generation on different surfaces, it's a bit hacky usually. I could probably just delete all autoplace settings/options from the underground surfaces, but then there wouldn't be any vanilla ores either. How do I decide which resources spawn and which don't?

I don't think I'll be able to fix this easily. This mod copies map gen settings from the "main surface", which is a setting you can change. By default it's set to Nauvis, so I don't know why Space Exploration resources are being generated if they're not generated on Nauvis.

I could set map_gen_settings.default_enable_all_autoplace_controls = false, but that would probably disable vanilla ore generation too. Autoplace controls are a complete mess in factorio unfortunately (that, or I just don't get it).

I do not know if that helps . I'm sure you will have googled too;-) Because I can't really test it, I'm probably not much help.
"autoplace_controls":
{
"coal": {"frequency": 1, "size": 1, "richness": 1},
"stone": {"frequency": 1, "size": 1, "richness": 1},
"copper-ore": {"frequency": 1, "size": 1,"richness": 1},
"iron-ore": {"frequency": 1, "size": 1, "richness": 1},
"uranium-ore": {"frequency": 1, "size": 1, "richness": 1},
"crude-oil": {"frequency": 1, "size": 1, "richness": 1},
"enemy-base": {"frequency": 1, "size": 1, "richness": 1}
},

That is a potential solution, but what about people using Angel's mods, Bob's mods or Py? I'd have to add compatibility for each mod specifically, which I don't feel like doing. For most mods, the default configuration is fine, it's just the mods that add surfaces like Space Exploration that cause issues.

The best solution I can think of is to specifically remove all custom ores from Space Exploration.

Something like:

autoplace_controls["custom-ore"] = nil

if this helps it sound good, I know myself with it unfortunately zero ;-)
I also mod a bit, but I haven't dealt with map creation yet.
feel free to contact me via discord kux#5599