Many cases and mainboards are just incompatible that way, as optical drives aren't all the same length, and it reduces the cost of the case slightly because of less material, if they make it so only the top bay is fully usable. Of course it's also somewhat the fault of the mainboard makers for putting components in that corner when making a full size ATX board. The narrower mainboards work fine no matter what components are there.
You either put up with the second drive sticking out a bit, or change the drive, mainboard, or case. It's difficult to tell for sure whether a case will actually have fully usable bays offhand, but you could determine what dimensions you'd actually need for a case to be in order to be deep enough to hold both drives. I'm not sure if optical drives generally have their dimensions listed online, you just need a shorter one.
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