well, if you are using native OS packages that would be one way to handle this outside of depending on any external system to track it and then you can query the os's tracking database to figure out what is installed. imo that is the preferred way.
you can use compliance for this too - you can write a rule that looks for the latest version of the software installed by file md5sum, etc and then if it's not there push the new version as remediation.
"I haven't seen a method that can be leveraged to bypass installing 'already installed' software without creating an enormous Script."
That's because there isn't any sort of out of the box integration to do this. As Bill suggested, it could be possible to deploy software conditionally using compliance jobs and auto-remediation. There would need to be an extended object in the template that fetches the version info from that database you're referring to, and then you could use the info in compliance rules to only apply the remediation (install the software) if the version to installed isn't already installed...
But that comes back to what you mentioned about creating enormous scripts...