Trying to create a 'ruined' aether portal structure, similar to the ruined nether portals added to Minecraft in 1.16

When generating the structure, whether by generating a world or using /#gen BrokenAetherPortal, a crater generates around with it.

I've tried to tweak the generation settings but cannot figure out what's causing this..

Here's the structure file > BrokenAetherPortal.zip

That sounds like you exported the structure with air blocks. I recommend looking up on the wiki on generating natural structures - specifically with natural floor and negative space blocks in mind.