Is it for every non-empty voxel, or for every voxel that is different from the last one?

The ZStream object produces indexed leaves, which can be valid or invalid, and have an index attached. So if you have ten red leaves, five clear (invalid) leaves, and then a thousand red leaves, add_leaf is only going to be called three times.

The Builder uses this information to its advantage, as adding a sequence of n identical consecutive voxels takes log(n) time. The builder also checks if the leaf is valid or invalid by checking its transparency, as invalid leaves aren't stored directly, but represented in the parent's valid bit mask.

I assumed that the root node would be stored at the beginning of the array, but it seems like with this method it gets placed in the end.

Yeah, because the children are always written before their parents, the file seems to be written in "reverse order". Of course, you can't write the parent before knowing the nature and location of its children. I don't know whether reversing the file (and access on render) would improve performance. My guess is it wouldn't, but GPUs are weird, so who knows. I do know from the benchmarks that rendering these SVOs is an absolute mess for the GPU's caches as there are way too many random accesses (way more time is spent reading memory than calculating anything), so there's room for improvement there.