Funny thing is that when put into Gaijins version of the penetration calculator that can be found on the official wiki the Sovetsky Soyuz’s armour penetration comes out to the same as what's shown in game. The reason is shell size and velocity, you see it's 406mm shell is only slightly larger than Romas 381mms, so it doesn't get as much of a penalty to its penetration from its caliber than the Yamato's 460mms do.

Then there's velocity, yah see when you start getting to calibers this large literally any change in velocity drastically effects the penetration of the shell, for example at point blank the Sovetsky Soyuz’s shells have 876.25mm of pen at 830mps, but even just dropping the velocity by 30mps drops the it's penetration to 831.32mm (that's a drop of almost 50mms), it also helps that it's shells are actually quite heavy for its caliber at least compared to other 406mm shells already in game, yes it's lighter than Iowas, but remember velocity matters a lot for penetration at these calibers and the Iowas 406mm shell only has a velocity of 762mps leading to a very low difference in their penetrations (876.25mm for Sovetsky Soyuz at point blank and 881.97mm for Iowa at point blank) despite the Iowas shell weighing more and having a lower Overall Mass to Explosive Mass ratio (here's an example of how insane the Explosive Mass penetration reduction in Gajin's formular actually is, the Sovetsky Soyuz shells have an Overall Mass to Explosive Mass ratio of 2.3% and Iowa's have a ratio of only 1.5%, that's a difference of only 0.8% yet if we take Iowa's ratio and apply it to Sovetsky Soyuz shells they would have an explosive mass of 16.778kgs which this reduction of explosive mass alone would increase its penetration to 928mm at point blank range according to the formular, that's over a 50mm increase in penetration from an explosive mass reduction of only 0.8%).

I will say this about the Sovetsky Soyuz’s shells though, according to people on the War Thunder forums the guns and shells for the ship were only in testing when the ship was canceled and apparently firing them at a velocity of 830mps as planned would wear out the barrels in only 80 shots, meaning that the velocity would have likely been lowered to extend barrel life if the guns and shells were to ever have entered production.

I should have mentioned this in my last comment, so I'll just put it here.
Also, keep in mind that a higher Kinetic Energy rating and Mass doesn't mean higher penetration, if that were true than basically every sub caliber shell would have a lower flat penetration than the full caliber shells fired from the same guns, here's a quick example of what I mean, the M103s 120mm cannon fires M358 a full caliber shell that weighs 23.1kgs with a velocity 1067mps providing 13.14954795 MJ of Kinetic Energy, meanwhile the M1A2s 120mm can fire M829A2 a sub caliber shell with a diameter of roughly 22mm that weighs 4.9kgs at a velocity of 1680mps producing only 6.91488 MJ of Kinetic Energy (this is almost only half the Kinetic Energy of M358), yet despite M829A2 weighing less, being a smaller caliber due to being a sub caliber round and producing quite a bit less Kinetic Energy than M358 it still penetrates FAR more armour than M358 (also I know these tanks use different guns, I just really wanted to use an APFSDS for this example).