Sorry for the noobish question but please bear with me. The motherboard I'm looking to purchase is 9.6" x 8.1" while the case motherboard compatibility is 12" x 10". Will it matter that the motherboard is too small or will it fit anyway?
If the board is a newer micro atx or regular atx, it should work. But to be safe, you need to research your case. BTX cases were produced for a short time mostly by dell and a few other oem manufacturer's. List your case type and model number. The dimensions you listed were the maximum size board the case can use. Most smaller boards will also fit.
Your motherboard will fit in the case since both of them have standardized mounting holes, all you need to do is match the correct hole of the mobo with the correct holes in the case and put the mounting screws in.
Since you have more free space in the case, I think it's better since you can get a lot of better cable management and much better air flow and cooling.
It's also a plus since it gives you more options for upgrades in the future and more free space for anything else that you plan to plug in later, also free space is easier to keep clean and neat....