I have created a document in version .92.2 with both the display units and custom size units set to px (pixels). However when I save as HTML 5 Canvas it converts the units to mm and saves it with that coordinate system (shrinking my drawing). I could see this being by design if the canvas specs where in mm but my research leads me to believe that the specs are in px.
Anyone else seeing this?

You need to set the 'Scale' value to 1, and then resize your drawing (it will shrink to just a quarter of its size, so you need to select it, lock the aspect ratio, and divide either width or height by the value that was in the scale field before you entered '1' there. This should give you correct values.)

You may want to open a bug report on launchpad for this:

https://bugs.launchpad.net/inkscape

I just made a simple test (I have Inkscape set for pixels). The size looks right, although I'm not sure how to know specifically what size the objects are, when viewing the.html