All true and yet, I don't see how any of that matters. The point of using the phone is it is something you have, and its not tied to the device you are connecting with. Yes, you may lose the phone more often, BUT...that just means you replace the phone and reload the software with a new key....BFD.
Stealing your phone doesn't reveal what systems you would connect to. Getting access to your laptop, doesn't provide the authentication token. Its about using two factors that are not tied to eachother in a way that a remote attacker can discern that improves the security of such a system.
which is why I strongly disagree that an app on the laptop is better.... because an app on the laptop is on the laptop, one device which connects to it all. Or another way to think of it...where is the safest place for the key to your safe.... in an unmarked envelope in your house....or in an unmarked envelope at your friend's house?
Even if your friend's house is less secure than your own, its still the better place because.... there is no way for the attacker to make the association needed to find it....even if it is your friend's house that he robs, even if he finds the key there!
Sure its not protection from specific kinds of attackers, but, if your security measures need to stand up to NSA levels of scrutiny, I have no problem declaring your requirements out of scope for this level of discussion, and far beyond most people who could benefit from simple tokens.