I know you posted this months ago. In case you or others are still curious.
When something is off center, then there has to be something wrong with the x,y positions in the code, for the top left and bottom right corners. Certificate uses the same native size images for all certificates but streatches them porportionally between the two points.
I looked at a certificate version in 2.9. The ../mod/certificate\type\letter_embedded\certificate.php file says the border for Landscape
$brdrx = 0; // the top left x
$brdry = 0; //the top left y
$brdrw = 792; //the bottom right x
$brdrh = 612; //the bottom right y
$brdrx = 10;
$brdry = 10;
$brdrw = 594;
$brdrh = 771;
You need to be able to edit the file or at least check it. As a fiddler of these files, I have been know to get confuzeled during the tweaking process.