Please excuse if I'm wrong, since I am speaking from experience with a MC Jubilee and a Graham 2.2, but I can see in that setup the very same visual discrepancy you describe with the A90/Phantom.
On the Jubilee there are three bumps at the top of the cartridge where it interfaces to the headshell. According to the Jubilee owners manual the purpose of these features are to provide approximately 2 degrees of azimuth adjustment.
What may not be clear is that the center ridge, that is the longer raised surface that runs partly down the middle from the cartridge front, is slightly higher in elevation than are the two raised bumps to the rear.
What this means is that the cartridge is intended to carry full contact, against the headshell, against the center ridge while it being optional as to which rear bump makes contact..... That means that Ortofon doesn't mind if one of those two rear bumps is not against the headshell.
As I take a close examination on my setup in use, it appears that, even though the Jubilee has two points of contact against the Graham headshell, the gaps seen between the low areas of the cartridge top surface and the headshell surface appear close to being uniform all over.
Fortunately with unipivots, azimuth adjustment isn't any kind of a problem. As to sra/vta, that's adjustable on the fly and none of us should have a problem dialing in that parameter even if your cartridge body isn't exactly parallel to the headshell....
I guess what I'm saying is; it probably wouldn't matter even if you did have enough headshell surface area to cover the three bumps, because the cartridge is going to be pressing its center ridge against the headshell and tipping ever so slightly to one side or the other.
-STeve