I am currently working on a resource pack that replaces quite a few of vanilla's structures. To do this I am using the structure void block to first load the structures I want to edit, modify them and then save them to my hard drive, from where I drag and drop them into my resource pack.

For the most part, this process works exactly as it should, parts of villages and the woodland mansion (the two structures I am currently working on) are replaced with my custom pieces.
The problem is how world gen deals with air blocks in structure files, or rather how it doesn't.

According to the wiki structure void blocks "[are] part of a structure and are ignored when the structure file is saved. This results in the blocks at the location where the structure is placed being maintained and not being overridden".

This works fine when I load the structure with a structure block, both air and normal blocks are set while void blocks are ignored, everything works as intended.

However, when a structure is generated by the world generator things are different.
Instead of behaving the way they should according to the wiki void block and normal blocks are placed while air blocks are ignored. This means that the places I want to be empty (e.g. interior rooms) can be filled with any blocks that were there before my structure was spawned while the blocks where I want to keep any previous blocks are now filled with void block.

Short version:

Current behavior when a structure is generated by world gen:

1. All blocks except air are set (including structure void blocks)

Expected behavior when a structure is generated by world gen:

1. All normal blocks are set
2. Structure void block are ignored
3. Air blocks are replaced with cave air blocks so that later parts of world gen can't generate inside my rooms

Steps to reproduce:

Modify a village structure and attempt to add a cellar using jigsaws and structure void blocks.