The alias used for Certificate does not have to correspond to the Private Key. So, you would have to take your chances.
Edit:
I haven't really tried this out. But it really shouldn't matter because a Certificate depends on the Public-Private Key. Password given in the keystore are just a way to secure them and giving it to only a trusted user. So, I would suggest you to generate the certificate and compare them with the other one's using the getEncoded method. This would give you the binaries and you could compare them.