How do I make it clear THIS generic NPC is a high level NPC?

...Cape.

Cape and fancy hat.

Yes.

I'm not sure how one is able to see through illusions simply by being more experienced and/or skilled, but game balance makes fools of us all. Maybe there's a specific way you have to squint that takes years to master?

In theory disguises added via ability, such as magic or sci-fi nonsense, is superior to having to lug around changes of outfits. The Outer Worlds had hologram disguises that I hated, however, so it's not a sure thing.

Granted, it undoubtedly depends on how they're implemented. In that game, you had to find a template for the disguise, it was automatically applied to you when in an area you were trespassing in, and you had a limited time to get somewhere before it would fail.

I didn't like it for a few reasons, but the big one for me was being put on a timer while trying to figure out how to navigate a place I'd never been to before (because of course I hadn't, it would have been trespassing). I'm fine with it being a problem if I lingered in one location, or got too close to someone with enough awareness to question my presence, but the timer was just "I would rather be doing so many other things than this, and this is supposed to be my fun free time."

As with many things, I think Fallout New Vegas handled this best. There's a lot gameplay-wise I would criticize NV for (while acknowledging the production challenges Obsidian faced), but its faction disguises just passively fooled generic NPCs, and you had to avoid getting too close to certain more competent NPCs if infiltrating a place, and that was great.