Good find! "Logically" they're pretty close, "emotionally" they can be different.
If her makeup is "over the top" that's a bad thing, she's not dressed appropriately. If her makeup is "extra" it's meant to be encouraging -- it's "over the top" but the "inappropriate" change is welcomed.
"Extra" is sometimes used with that sarcastic element or downward twist (seen by OP) that chips away the welcoming bit. In that context, I think the usage is similar to "over the top".
If her makeup is "over the top" that's a bad thing, she's not dressed appropriately. If her makeup is "extra" it's meant to be encouraging -- it's "over the top" but the "inappropriate" change is welcomed.
"Extra" is sometimes used with that sarcastic element or downward twist (seen by OP) that chips away the welcoming bit. In that context, I think the usage is similar to "over the top".