The reason has two parts:
As you know, valuable resources become progressively less scarce as you go deeper, especially below lvl 30. Within those 30 levels, things like redstone, diamond, lapis, draconium, etc., occur even lower (below lvl 10). So, if you quarry horizontal slabs top down, you will have to wait a bit before the really juicy stuff starts showing up in your collection box.
Also, quarrying uses a lot of power.
So I set the Builder up to quarry in the Deep Dark.
1. I'd like to define a long block, say 30 wide, 30 in height (from lvl 30 to bedrock), and 1000 (or more) long.
2. Then I want it to start at one end of the length and work its way, in vertical slabs, to the far end (1000+ blocks away).
3. I can remotely start/stop the quarrying from the Overworld.
4. The quarrier would then quarry the first vertical slab and give me a full cross section of what's available in a 1x30x30 vertical slab - so I'm more likely to get some redstone-level stuff in the first 90 blocks quarried. If the slices are horizontal, a lot of RF will be used to get stuff that's less valuable first.
Also, with horizontal slab quarrying, I'd have to nip down to the DD every so often to set up a fresh block. With vertical slab quarrying, I could set the block up once, and have the quarrier just start at one end, stopping and starting on my remote command.