I've written a simplistic Python script [1] that will change all of the font-size units in an SVG file from pixels to points. The script doesn't actually do a conversion it simply replaces the unit suffix of px with pt.
If you create some text in Inkscape with size 10 and save it; font-size:10px Run the script on the file; font-size:10pt Open and edit the file in Inkscape; font-size:12.5px
This is a workaround for the bug that the UI never shows the units (pixels) associated with font size numbers and it is difficult to specify sizes in units other than pixels [2]. This is the quickest hack I could put together when I realized that the text in all of the figures for my thesis was the wrong size, therefore it hasn't been tested much, so if anybody uses it you should take appropriate precautions (e.g. backup your data).
Clearly this is an ugly hack, but if there is no interest in fixing the underlying issue, or it's to painful, I could put together something similar as an effect. It seems like a better solution would be to, at a minimum show, what unit font size is in. When setting the default font size in the toolbar specifying a unit results in the correct conversion, so maybe a more general fix wouldn't be to hard. Unfortunately, trying to specify a unit when changing the size of existing text or doing anything with a unit in the text dialog doesn't work. In any case, I would be interested in getting some input from others.
Best,
[1] http://www.unm.edu/~jdfrech/svg_font-size_px2pt.py [2] See bugs 161347, 1619753, and 1657337
P.S. Sorry about the cross-posting but this seems like a somewhat nonobvious issue that has tripped up at least a few other people before me.