Chris Wraight has placed a pretty clear reference to the Khan vs Mortarion at the Lion's Gate back in The Carrion Throne, so I'd wager that duel is inevitable. The question is one of when, not if.
The two door faces were embossed with beaten ceramite, sculpted into representations of the battles that had taken place. Idealised Angels of Death clashed in bas-relief, their blades glimmering under an accumulated patina of ages. In the very centre, where the immense bosses swelled out, were two greater figures – the Holy Primarch Jaghatai Khan, and a nameless daemonic monster wielding a scythe.
I was sort of hoping that would be Wraight playing with history and the two never actually coming to blows again. I'm down for either, though I think there are far more interesting places to take their dynamic than yet another primarch brawl. Otherwise I'd rather see him try Fulgrim.
But if they do meet face to face I hope Jaghatai gets thrown into the webway or something.
I think something pivotal as two Primarchs duelling during the big Siege, after which the Palace would be in for some... remodeling, is precisely the sort of thing that would be captured in art around the location of the battle. Seeing that it even depicts Mortarion with a reasonable degree of accuracy, looking at Manreaper, it makes me think that no historical shenanigans would be afoot here. If they wanted to depict the Khan fighting a daemon Primarch, it might as well have been Fulgrim, or Angron, but the artist chose Mortarion.
For me, it's enough to think that present day folks have no idea who Mortarion is anymore, and thus look at the murals in confusion, recognizing only the Khan. That's a figure they've been told time and again to worship, after all, while the enemy Primarchs were pretty much forgotten about. There is no need to additionally make the depiction factually incorrect, especially when it was added to the Lion's Gate back when rebuilding happened, which might have even been under Dorn's supervision before he left Terra. At least I doubt he'd have just taken his Legion and left with the Palace's defenses basically broken, and it may also have been a cathartic experience for him to be rebuilding some of the more vital structures and putting the bling back - remember, he always at least claimed he would be putting everything back the way it was, once the war was over.
It's a fairly safe assumption that a lot of those memorial statues and what not were commissioned or produced at least during the time when the Primarchs were still around, and Guilliman took control of the High Lords for a while. Terra was properly rebuilt during the War of the Beast, at the very least.