Only one method can be used to pay for metamagic feats that affect a single spell.
The context of this statement from the feat’s Special section is about paying for metamagic partially with a higher-level spell slot and partially with bardic music uses, but the statement still exists and isn’t actually qualified: only one method can be used. Using Metamagic Song twice is paying for the metamagic feats two ways.
This is consistent with the quoted limitation on Metamagic Song, which says that “feats,” plural, cannot be used with Metamagic Song if they would, combined, raise the spell’s level above that which you could usually cast. That implies that all metamagic feats applied to the spell must be addressed through a single use of Metamagic Song.
This can still be cheesed around, though: Talfirian Song from Races of Faerûn allows you to make an illusion count as a higher-level spell, up to 9th level. Thus, with that feat, the “highest level of spell you can cast” is 9th, assuming you have an illusion spell and enough bardic music uses to heighten that spell to 9th level. Now, it does say “the highest level of spell you can cast normally,” which is always a contentious thing in 3.5e: for the most part, “normally” means “without this effect,” which means using Talfirian Song can be part of our “normal.” People often want “normally” to mean more than that—that it refers to some base case without considering various effects—but this isn’t supported by the rules, because no such base case is actually defined, nor are the effects that count and the effects that don’t. So rules-as-written, this works; whether or not your DM will buy it depends a lot on the power level of the game overall.
