I don't have the code/configs in front of me, but if i remember correctly it was a collision/comprimise between...
1. the default if there is no <dataDir> is to use "data' in the instance dir
2. that the legacy behavior of <dataDir> was to be resolve the path relative the working directory (not the instance dir)
3. that people wanted to be able to use a solr.data.dir property with the example configs to pick an arbitrary data dir at run time for demoing stuff.
...if we comment out <dataDir> then #3 stops working. and because of #2 it's impossible to have a default for the solr.data.dir property in the example configs which matches the same behavior as having no dataDir at all.
we might just want to bite the bullet and say that in the next version of solr, dataDir will be relative the instance dir, and if you don't like it add some new 'rel="cwd"' attribute to the <dataDir> tag. (or add a new default system param for absolute path of the current working directory and tell people they have to use that if they want the rest of hte value to be relative that directory)