Like I said on Discord, I wonder if it's an idea to add a switch to allow/disallow structure void to be pasted - I can see it being useful to know where they are

By default, Structure Void blocks should be pasted because they are simply part of the structure / schematic, I think.

In vanilla, structure_void is like the //paste command flag “-a” from FAWE, but “-a” affects air and structure_void would remain. So the vanilla behavior is exactly the opposite of the FAWE behavior when using "-a".

Maybe a paste command flag for FAWE would be an idea, which would paste AIR like in Vanilla and leave out structure_void blocks. Anything else would perhaps be unusual.

Just ran into this issue saving Minecraft structure schematics for my plugin, would appreciate this getting merged!

Should be fine now ig.
Saving a structure with structure void blocks doesn't save the structure void blocks in the palette or block compound (they are ignored). This seems to be consistent with the actual Structure File format, as I haven't found any builtin structure file which actually contains structure void blocks. I would guess they are simply ignored as a whole, which fits structure void blocks.

When loading Structure File clipboards / schematics the resulting clipboard is filled with structure void blocks, so that every clipboard position actually has a block. Known blocks are overriding the structure void blocks.

Pasting without any arguments pastes the clipboard including the structure void blocks (suitable for knowing where they are of if the structure needs to be changed). Passing the -v switch (e.g. //paste -v) doesn't paste structure void blocks (inverse block type source mask) and keeps the target block unmodified (the one which would've been overridden with the structure void, kinda like -a). That should follow the spec as described in https://minecraft.wiki/w/Structure_Void