However, I wanted something with at least 6 SATA ports as well as more than a single PCI-e slot for future expansion.
There are other options than cheap Atom boards (Atom and otherwise - based on the rest of your post, you haven't seen all low-power options)... but they're not as cheap. Your mainstream board makes more sense in that perspective. It's not low-power but it's not always rational to pay more to get low-power parts.
I also wanted something with integrated graphics and integrated RAID support
Virutally everything has integrated graphics nowadays.
Why do you want integrated RAID if you're not going to run Windows? I don't get it.
For the PSU, about the only way to go more efficient at low draws is a PICO
75% at 25W is pretty bad. It's not that hard to do better.
But you may be right in that it's probably not worth the cost (you might as well buy a low-power board instead).
At some point I do plan on an ARM NAS to add to my network for ultra low power media streaming, but it isn't going to come close to slicing my bread for what I need for file serving and backup duties (and I may do web serving off the box at some point as well).
You may not be aware of what ARM can do nowadays. ARM can definitely pull off fast file serving, a little web serving and mundane backups. But the cheapest ARMs are not that good. So once again, a watt-guzzler may be cheaper for what you want to do.