agreed each product checks differently and so your results vary and each have their own pluses and minuses.
Nessus seems to check the files and care less about actually "installation". I see them looking at more file version numbers listed in the KB than registry keys indicating something is installed.
They haven't been far off on most of the results. They also alerted us to situations where we removed a legacy installation and files were still remaining (and potentially loaded as it was under the windows folder).
FYI, i do NOT work for nessus. Just seems to be a solid way to verify the environment. With the landesk agent we rely on the deployment and the agent reporting in. I like to have something agentless that scans all the endpoints as well.