No problem with E-ATX in my experience.I only have experience with Supermicro micro atx boards which fit fine. It seems that E-ATX boards are the ones which have an issue.
I know this is a somewhat old post, but what size drill bit and tap did you use to create those motherboard standoffs?I have the SM X10Dri-t myself. I fit it into the thermaltake urban t81 chassis by drilling 2-3 holes. Not a difficult task at all if you have the powertool and some basic skill.
Thermaltake - Urban T81