Because he saw him in the past, doesn't mean that he is reletad to him. Tho, I suppose it's possibility, but I doubt, since Urahara never showed any goodly powers like Yhwach.
I writte numeros times my theory that both Aizen and Urahara were in RR in the past.
I doubt it, no proof of that yet.
And explaining urahara current status is simple.
"Knowledge is power"
That's clearly what aizen and yhwach have that make them surpass others.
i think urahara's character is just naturally mysterious. think he's a read herring in a sense. meant for us to think he has underlying malicious intentions, but thats just the way he is.