I think they might have meant her submissive nature instead of looks. The mom had been entangled with a man that had put his work above her, and I'm taking a little creative liberty here, but I think their dynamic was that she easily submitted to him because of his crafty nature and the fact she was too timid and scared to fight back, in a way like how the ML and FL's situation first started (him blackmailing her to marry him.) The type of person that if someone's forceful, they'll easily back down. This idea was confirmed by them when she easily agreed with their terms to leave the ML.
Towards the end when the ML cuts ties with the dad, the secretary is probably reminded of the mom again from the contrast of the ML's forceful nature towards the father and the FL being politely quiet in the background (despite the things the father's done), even bowing to them before she left. She takes this as her being timid and submissive like the mom, but the father corrects her in saying that they're not alike at all, noticing that despite her reserved and kind nature, she won't back down for the sake of her own happiness and what she wants, unlike his deceased wife.
I actually agree with this statement that she isn't as submissive and quiet as we were led to believe. In the beginning she isn't able to speak for herself, but throughout the story you see how vocal she is towards what she wants in bed and has even gotten after him for doing things she hasn't agreed on first. Really refreshing to see this compared to other FL's in this type of genre. (▰˘◡˘▰)
this was cute and everything but what did tusneyasu's secretary mean when she said that FL resembles ML's dead mom???!!!!!! why can I never escape Oedipus complex???!!!?! im gonna cry, just when I thought I forgot it, it came back, and so unexpected too