Not actually, I am thinking of using the 1 PCIe 16x slot and another GPU connected to the 1 PCIe1x slot which should be more easily available. That's why I am looking for such motherboards. Does it make sense or am I missing anything?
If you are not planning to invest in 2 GPUs right away then I would advise you to go for a motherboard with only 1 PCIe 16x slot. Since, I know in certain local stores the price difference between a motherboard that has support for 1 slot as opposed to a M/B with support for 2 slots is way too much.
Instead you can save on that much money and invest it in a more powerful PSU which you can use later even with 2 GPUs.
The price difference between an ASUS M/B with 2 PCIe 16x slots and the one with only 1 PCIe 16x slot is 2 times. It just depends on where you are located and what boards are available.