Since there probably are a lot of implementing parsers out there, I figured it might be better to filter the line separators in the core parser itself than from the wrapping parsers. Attached is a patch of my workaround for the inconsistent line separators. It modifies MXParser.getText() and a test method is added too.
The patch doesn't involve any doxia code, but I hope it helps resolve this issue. 
Fixed writing of \n, now we need to process the Strings passed as parameters and change the line endings to the current system' one