Branding?.. no... I think its been that there has been no need for it to make our tools work as desired.
The beauty of our tools is that its all open-source though; nios-convert calls format_conversion_utils.pm (located within the quartus installation); you could just add the necessary functionality to it and share it here for all to see ;-)
Also I was serious about google -- while doing some recent work I came across an s-record to binary converter with 2-3 minutes of searching which I just downloaded and used for my needs at the time....
On your question about quartus conversions: yes, all (I believe) Quartus utilities are scriptable and available via the command line. quartus_cpf is "convert programming files".