I vote #1
I think #2 or 3, if you go that way, should apply unilaterally across all metamagic feats. You are modifying the base spell regardless of what the final product is. It's also cleaner than trying to divvy up which feats this applies to. I also don't think SR is easy to overcome until high levels. For a 6th level caster, it sucks - as demonstrated by Drax's 0% success rate vs the deva.