It's because there's a number of things that increase in cost rapidly to get something similar to the enthusiast build in the OP.
ITX boards have crappy sound, so you add on $100 DAC that would otherwise be included in a $200 mATX/ATX mobo. ITX cases need better fans to cool parts that draw more power, so you add $30 there. It all adds up quickly to be about $300 more than the comparative mATX/ATX build.
And yeah, it needs to be updated
For RAM, just get the same stuff listed in the OP. Low profile.
Here you go
Just make sure you have positive pressure, as then the only way air goes in to the case will be through these filters.