I'm confused by what you are asking, of course the board will fit and work, it will fit on any board with a PCI-16x slot, be it ATX, mATX or ITX. Will it cover up the bottom PCI-E slot? yes, that doesnt make it completely unusable though. Like if you were going to use that 2nd slot for expanded nvme storage, you could just use a small rise cable to make the slot usable again (I did this before, where i used a small riser cable to mount my nvme expansion card at a 90 degree angle to the slot.
In my current build i have a 4090 connected to a x670e-i ITX board.
What are you attempting to do with the 2nd PCIE slot?