The reasons you provided were all in situations where physical combat was involved. Urahara has the means to keep this a ranged battle which considering he has better kido and equipment he would come out victorious. Unohana would stomp him in combat however since he has like 1 on panel combat feat against Ichigo when he first got his shikai.
But Urahara has to engage in some kind of direct, physical combat because his shield has to appear right in front of him (as Unohana brings down her sword) and his Tsunappe involves direct contact with whatever he's trying to counter. These are all close-ranged Shikai techniques.
The only thing Urahara can do against Unohana is Juzutsunagi or use his 91 Hado. Even if Unohana gets caught in the net, it wouldn't kill her because of her incredible healing Kido. She'll just restore herself every time. And the 91 Hado is only good if Unohana is restrained. There should be no reason as to why Unohana, a master at Kido and at physical combat, should not be able to break the Bakudo used to restrain her like Aizen.