First of all, I would like to warn that discussing or downloading security sectors (ss.bin files) from the internet is not allowed on these forums. These files are copyrighted by Microsoft, so we can not allow help with such. Since you did not link to the site, I will leave this thread open. Just realize that nobody here will be able to help you with any downloaded games or ss files.
As for your questions...
The checks by SS Merger rely on a database. This database is only possible with user feedback. It is an incomplete database. In other words, you could have the correct ss and the correct dump of your game, but both boxes will remain red because perhaps nobody has confirmed either of these yet? Please realize that the database is also hosted on the internet, and last I checked HellDoc can no longer host the database for free (the database may no longer be updated for all I know)
The only way to know for sure is to make sure you have a correct, full dump via hotswap and extract your own ss from the original disc.
To extract the SS from a Hitachi drive: connect the drive back up to your PC, get in ModeB, use Xbox Backup Creator's drive tools tab with your original disc to extract the ss
To extract the SS from a Samsung drive: connect the drive back up to your PC, get in 0800 mode, use Xbox Backup Creator's drive tools tab with your original disc to extract the ss
