Where do you get this from btw? I don't remember her being able to do that. And why would atomic level destruction become selective on something such as durability?
Coming off how Bluebeard's abomination and Rider (Medusa) were killed off with Excaliblasts. Those with some means of magic resistance such as Gilgamesh's golden armor would be able to resist the atomization effect from Excalibur.
Sharingan + Rinnegan = GG.
If prana's being equated to chakra here, then this would make Saber immune to mind manipulation and her instincts could not be fooled easily by illusions. This would also allow Lancer's spears to pierce Susanoo since Gae Dearg can pierce through magically-enhanced defenses such as Saber's armor.