I would expect the dual-ISO shot to be a touch better. Because you clearly haven't ETTR the lower ISO and the higher ISO will now be ETTR. Of course, you could have just ETTR the low ISO and called it a day 
Thanks for your patience on providing a number of clarifications.
Based on what you've written, there doesn't seem to be much, if any, downside to having Dual-ISO enabled all the time. With static images, you'd take the time to get ETTR at a good setting.
If I understand what you've written, with a low to moderate contrast scene (as evidenced by fitting within the histogram), most or all of the information would come from the low ISO part of the exposure. The high ISO info wouldn't apply.
But when you did need the expanded DR of Dual-ISO, it would be there.
Somehow, I think that conclusion reflects a simplistic understanding on my part.
And to me, a more complicated and slower workflow is a liability (not a limitation, as you point out).
Some geek speculation:
The impression I have is that during the actual exposure, a ML routine is invoked that examines a pair (or quadruple?) of scan lines. In real time during the exposure, it is deciding whether to used just the low ISO pixels, or to merge the high and low ISO info. It almost seems like that would be on a pixel by pixel basis.
But I have my doubts that is really going on.
Also, I'm unclear how "aliasing" comes into it? Do you have a situation were two (or four?) pixels are averaged and/or interpolated? I observe that the thumbnails have a huge amount of moiré, but that's gone after cr2hdr.exe works its magic.
But I guess I don't have to understand how it works to be able to use. Whew.