A "stacked" belt goes in, a flat, single-high belt comes out, and total "output end" throughput (all outputs) appears to line up to the number of input stacks, not the number of input items.

Ah! That should work, I'll check it out - thanks for the report.

I've looked into this - it appears that stacks are flattened during underground transport but items aren't lost. If you click on the output port you should see each input stack ticks up the inventory quantity by your stack size. I agree stacks should be preserved though, that seems like the more correct behavior. That adds complexity into the "max buffer amount" calculations that determine how many items the network can hold based on the distances between ports. I'll investigate fixing this but don't have an ETA at the moment.