Hi,
SAML doesn't do any password stuff, it's authentication from a central point. This means if you're using SAML with Yubico's server, there is actually no password (the OTP generated by your Yubikey is validated on the Yubico server).
If you're wanting to login from your iPhone you will need to set your password in Google Apps.
The plug: We actually have a solution the integrates Active Directory password changes into Google Apps. This also has SAML capabilities, but at present does not have Yubikey OTP support. If there is sufficient demand, we would certainly look at implement this.
* Sufficient demand would be a client with several hundred users (we're used to dealing with enterprise and education).
http://www.totali.co.nz/