58846 vs 58946 refer to setting up @binhex's VPN apps in either VPN mode or normal mode AFAIK. You could term it a false positive, since that's how it's suggested to set up the apps (by removing one of them). It's been previously suggested to me to put in a special test for binhex templates and I have elected not to because IMHO if the ports are listed in the template but not on your installed app, then it is an error / warning. That, and its easy to ignore (IE: don't want to go down the road of having checks for individual apps where its perfectly acceptable and even desired in some cases to set it up as such - I just don't have that much time on my hands)
The extended tests are basically full file system checks - permissions, duplicate filenames. What you wanted to hit was "Re-Scan"
These are the warnings / errors that are ignored that are found in the last scan
This is the list of ALL errors / warning that you've ignored, regardless of whether its found on the last scan or not. It's there to let you re-monitor an error that you've previously ignored, it isn't currently present, but you want to be alerted for should it happen again.