So the whole point is to approximate the reference pixel by doubling your device pixels (or tripling, or whatever).
I think you may be thinking of a different definition of CSS pixel that used to exist a number of years ago (when "px" and reference pixels were the same thing). That definition is no longer in the spec, and hasn't been in a while. And that's precisely because of the antialiasing issues you mention.
Yes, the official W3C recommendation changed to CSS2.1 earlier this year, and they did effectively redefine a CSS pixel at that stage. I'm not sure this did more than swap one problem for another, though: as I read the (current) wording, we shouldn't get fractional physical pixels any more and basic arithmetic still works on pixel lengths, but now you can only scale up by a factor of 2x, 3x, etc.
Given that the point we're debating here is the merits of setting a minimum 16px body text size, that would mean the next alternative was 32 physical pixels on a display of roughly 200dpi resolution. While that might be useful, you could still find that depending on the physical properties of your devices, 16px text needed to render at say 24 physical pixels to look the same size to the reader.
When you've got that kind of uncertainty to work with, I stand by my earlier comments that an arbitrary 16px size without reference to either the specific font or the physical properties of the device isn't a particularly useful guideline. The design considerations for devices with such different physical properties are too complicated to dismiss with a simple scale factor.
The definition of CSS-px (for low-res devices, which includes all the mobile stuff so far; high-res in this context is print) is:
and the reference pixel is defined as: See http://www.w3.org/TR/CSS2/syndata.html#length-unitsSo the whole point is to approximate the reference pixel by doubling your device pixels (or tripling, or whatever).
I think you may be thinking of a different definition of CSS pixel that used to exist a number of years ago (when "px" and reference pixels were the same thing). That definition is no longer in the spec, and hasn't been in a while. And that's precisely because of the antialiasing issues you mention.