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Thanks for the patch.
I think the extra check should be done unconditionally in the case where we've looked up the default .netrc file. Adding a feature to 3.3 to provide an optional check for other files (with default False) would then be an additional enhancement, and I think a good one. That should be a separate patch, probably even a separate issue.
I don't think the parse error is the right thing to raise, but I'm not sure what is. An OSError, perhaps?
I'm adding the 2.6 release manager to see if he thinks this is of sufficient importance to go into a 2.6 release.