@Nitroraptor53, I don't know if you're still pursuing this, but I did a bit more digging into the Elan SC520 and discovered a couple of limitations. They don't make it completely unsuitable for a MicroATX build, but they are important to note.
First, the SC520 only supports two ISA DMA channels, but can be numbered as desired. A typical 486 gaming PC would use at least three: 1 and 5 for a SB16, and 2 for the floppy controller. If there's a ECP/EPP parallel port instead of just a standard bi-directional LPT port, that would normally use channel 3. Strictly speaking, a modern system does not need a floppy drive, although a 486 usually has one. There's always SHSUFDRV for making a virtual floppy drive in software. It might even be possible that a floppy drive and the sound card could share a DMA channel, especially if they are not going to be used simultaneously. As for the parallel port, ECP and EPP are nice to have if you're plugging in a Zip drive or scanner, but again, not really crucial. PCI LPT chips exist and would side-step this issue.
The Elan SC520 Customer Development Platform we talked about earlier has a Super I/O chip with a floppy controller and an EPP parallel port wired to share one of the two available DMA channels.
Edit: Looks like I misunderstood. The SC520 supports four ISA DMA channels. The SC520 Customer Development Platform dedicates two of those four to the Super I/O chip and the IDE interface (see page B-4 of the manual.) A 16-bit sound card would use two channels, which would leave none free. To spare one more DMA channel, using a PCI IDE interface instead would ensure that the second of the two ISA slots has a DMA channel available.
Second, the SC520 does not support ISA bus mastering by expansion cards at all. The MASTER signal is completely missing. ISA SCSI cards and the like would not work, although PCI SCSI cards would work just fine.
The takeaway here is that the Elan SC520 can be the basis of a nice 486-class gaming PC, but it won't have all of the options that a typical 486 motherboard has. If the goal is to make an "ultimate" microATX 486 motherboard that is all things to all people, then the Elan SC520 is not suitable.