I think this report can be closed. The issue appears to be that the program in question (or the installation steps that accompany it) do not conform to Debian's policies or the insserv/startpar approach to doing things.
If someone submits a patch or writes a companion tool to scan for new, unidentified init.d scripts I'll be happy to work with it, but I'm not seeing a strong case here for adjusting behaviour to deal with scripts that do not follow Debian's installation steps (ie using update-rc.d). - Jesse
