Bonuses to notice you are just that. Bonuses to notice you, not to pierce a disguise. Because they can only attempt to pierce a disguise once they notice you. Get it?
So if you’re walking around in an outfit that doesn’t stand out with a skin color that doesn’t stand out, they don’t get a bonus to notice you. If they did notice you they would get a second roll to pierce your disguise, but if they can’t make that roll in the first place the quality of your disguise doesn’t matter.
The effect of the Charm is that so long as you make some effort to not stand out you won’t. Wear something that could be confused with a guard’s uniform, have a hood up so they can’t see the color of your skin, don’t have a giant golden death-surfboard hanging from your shoulder or be covered in the blood of the last five guards.
Note that your disguise’s skill doesn’t much matter. In fact, a very good disguise could work against you here. If you, say, disguised yourself as a beautiful courtesan then the guards may get a bonus to notice you because beautiful courtesans want to draw attention to themselves. The same is true if you disguise yourself as somebody famous or that they should know: disguising yourself as the local warlord probably nullifies your stealth because everyone gets bonuses to notice him since he’s kind of important.
(Addendum)
Do me a favor and turn to page 128 of the Core Book under Disguise.
Note how the rules say there is a difficulty for trying to disguise yourself in certain ways? Like +1 for a person of a different gender, +1 for racial background and +1 for body type?
Those are basically your “You stand out” traits. So, to not stand out as a Northerner in the South you need to make a Disguise roll at +1 difficulty. If you make that roll, you are disguised as a Southerner. The extra successes beyond this determine how good your disguise is and whether it would fool people, but at that point your disguise was successful. Similarly, if you were trying to look like, say, a official who has every right to be in an area where only officials are allowed, you would need to acquire the various props and gear appropriate to that disguise, otherwise you would need to add +2 to the difficulty of your roll.
Let’s say you are a Western male overweight Solar trying to sneak into an area that only Brides of Ahlat are allowed to enter. You don’t have any sort of props or gear. So you would need to make a Intelligence + Disguise roll at +1 for wrong gender, +1 for wrong ethnicity, +1 for wrong bodytype, +2 for no props or difficulty 6. You would need to roll seven successes on your roll. If you get that many successes, normally the opposition would only need two success on the reflexive Perception + Awareness roll to pierce your disguise since it’s only a one success threshold which means that despite being amazing it’s actually also kind of poor.
But with Easily Overlooked Presence Method, that never happens. You’ve successfully disguised all your “I stand out” traits and can breeze into the Temple of the Bull God and make off with some relics.