Mini ATX board too weird in ATX mid tower case?
An mATX motherboard is just less tall than an ATX motherboard. It will just not reach the bottom of the case, there won't be pci-e or pci slots on the motherboard to make all openings in your case useful for something.
It may look a bit ugly with the usb 3 cables and front end audio cables being visible if you don't route them through the back of the motherboard some way, but other than that I think you'd be able to tolerate it and not even think about it.
It will look similar to this picture... but will actually look even better because you'll have that shroud over the power supply, across the whole bottom, so it will make the case look less empty.
actually here found a cougar 330 atx case picture and resized motherboard cut from the picture above to show how it would look :
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