If you mean pads for dampening sound, I expect you could fit a layer of Dynamat or similar in there behind the plastics. I would have conserns about heat doing something like that though.
I believe adding heatsinks to the chipset can be beneficial when overclocking (especially the system bus). It certainly won't do much harm if you do it right (supergluing bits of metal onto chips is not advised for example). The memory controller in particular will get quite warm in some systems.

The motherboard should sit happily on its standoffs. The build quality of Apple's cases is second to none. You needn't worry about shielding the back wall of the case.