I think that trait can only be used ONCE. That planets and space stations within your territory at the time the trait is acquired will flip. That's the only way I can explain having the trait, but planets and stations that later get drowned in my cultural expansion do NOT flip.
Yes, but you can time it just right. Remember you don't have to spend an ideology point immediately ... so you could, if you really wanted, really lay cultural starbases on thick to capture everything you want, drown out as much as you can. You could flip an entire civilization out of existence.
And you don't even have to play Benevolent ... the trait is only 3 tiers in so you could snipe it.