Good question, but as has been pointed out in this thread, "Almost all motherboards" are not destined for use with double wide graphics cards.
Why do motherboards ship with an x1 slot below the x16 slot? The simple answer is "Flexibility"... if its there for you to use, you may use it.
Now, don't stop asking questions--that is after all, how you learn seek answers and increase your geek quotient.
But take a moment to think through the alternatives to your question.
[*] If they replaced the x1 slot with an x16 slot below another x16 slot - Wouldn't you be here asking "why are they placing a second graphics card slot below the first?! I cant use it if I use a double wide!"
[*]If they left a blank space beneath the x16 slot (and some motherboards do), wouldn't someone else who uses a single slot graphics card say "why are they leaving a blank space below where I could use another card?! This is a waste of space!"
[*]And what if they're like me? Given the prevalence of dual slot coolers on mid to high-performance graphics cards these days, I want an EXTRA SLOT's worth of space after the two taken up by the graphics card. I want the space for air to flow in to feed the fan, I dont want one graphics card trying to breathe in the next card if I use a dual-card setup. Don't you think I've been looking at current motherboard designs and asking "Why the hell are they putting the two x16 slots so close together? They should stick more x1 slots or empty space between them!"
But you can imagine...that wont do for everyone, especially people trying to cram 3 or 4 GPUs in their systems.
....the real answer from all this is that everyone has different needs from their motherboard. The best thing Mobo makers can do is to try and populate all (or most) of the available expansion card space with slots, then vary the arrangement throughout their line, hoping that each of those arrangements will align with the way a couple of different people want to build their system. After all, you may not need an x1 slot there, but its much easier for you to not use a slot you don't need, then it is for someone who needs a slot to not have it at all.