In the description of Metamagic Song from Races of Stone it includes the line, emphasis mine:
Applying metamagic spontaneously using this method increases the casting time of the spell normally.
This confirms that the increased time for applying metamagic to an spontaneously cast spell still applies.
If you didn’t use Metamagic Song you can use Rapid Metamagic to reduce this to “its normal casting time”.
Can you still use Rapid Metamagic if you use Metamagic Song to payoff the cost?