D&D 5E Greater Invisibility and Flanking?

[Oofta]

That sounds like a character using metagame knowledge to determine their course of action. How do they know that leaving themselves open against the invisible attacker doesn't make them any more vulnerable than actively defending against them?

How does the PC know anything? All they know is that they can't see where the attack from the invisible character comes from. If you can't see where that attack is coming from you may as well do your best you can to avoid attacks you can see.