You can disable onboard sound and video on most motherboards that have either, and then put in add-on video and sound cards.
The motherboard you've listed is a decent board, (though it has onboard sound and ethernet, not too unusual today). I prefer motherboards by Asus, but that's personal preference, there are probably people here that would prefer MSI, as they are a good brand. One point: I'm not a fan of VIA chipsets, after having some AGP 4X issues with one of their older chipsets. However that's a personal bias, you should ask around here what other AMD users would pick for a good motherboard/chipset, you'll probably get some good advice.
That case is 20.9 inches high x 8.1 inches wide by 20.5 inches deep. Use a ruler to imagine it's size. It's a nice sized case, and it is pretty easy to cool that particular tower. (I was looking at those, in fact, around 6 months ago, still haven't decided what my next case will be though).
If you're getting an Athlon64 and a decent video card, then you want a decent motherboard to go with it, and the VIA chipset boards are certainly NOT king of the hill ;)
Find a motherboard with an NVidia nForce3 250 chipset on it, and forget about worrying so much about what features it includes. You can disable the ones you don't want. By the way, I haven't really come across any such boards with onboard video, so that shouldn't be a problem.