Not per-document yet, but better than nothing...
For specialized uses, several aspects of Inkscape's SVG output can now be customized via editing the preferences.xml file (there's no UI for these options). A <group id="svgoutput"> inside <group id="options"> can have the following attributes:
* usenamedcolors (default is 0). If nonzero, Inkscape uses symbolic color names (such as "white" or "lime") and three-digit color designations (such as $dfe) where appropriate; otherwise, it always uses six-digit colors (such as $d0f0e0). Note that in 0.44, the default was to use named colors, which created problems for some extension effects.
* numericprecision (default is 8). This is the number of significant digits written for each number into SVG. You can lower this number to get slightly more compact SVG at the expense of precision.
* minimumexponent (default is -8). In transform= attributes, any number whose absolute value is less than 10 to the power of minimumexponent (i.e. less than 10-8 by default) is written as 0.
* indent (default is 2) controls the number of spaces that each level of nesting in SVG is shifted. Set this to 0 to disable indentation.
* inlineattrs (default is 0). If nonzero, attributes are placed on the same line as their tags; otherwise they are separated by newlines.