delay on capship colonise bonus

could you provide more specific details?   

He could have articulated better but I know what he means. Let's say I have a level 5+ Advent Mothership with level 3 Colonize, for a 60% cost break.

I colonize a planet. If I try to build enhancements now, I pay full cost. Instead, I have to wait a while (I haven't timed it, but it's around 30 seconds or so) for the price break to kick in and I pay 40% instead.

It's hardly game breaking, but it's really rather annoying to have to colonize, then go do something else, then come back to it later for upgrading rather than the more natural colonize -> upgrade -> go do something else.

Yes, I'm guessing it was left over from when colonizing took longer. Basically every colony capital applies its colonizing bonus some time after colonization. It's not a big deal in the case of TEC that get free extractors, since you can simply queue the 1 or 2 less, but for Vasari/Advent you do have to sit around and wait for a bit twiddling your thumbs before being able to take advantage of it.