I know you already know about this bug, but I figured since you said you didn't understand it, I'd let you know why it's happening.
Because RoadGenerator is a surface populator, the same kind of generator as the one that adds the flowers to the world. As a result, it is likely that the flora surface populator is running before the RoadGenerator (and it generates based on what block is below the potential flora which will be grass when it runs), so the RoadGenerator is replacing grass blocks that already have flowers on top with asphalt, breaking the flowers.
I know you already know about this bug, but I figured since you said you didn't understand it, I'd let you know why it's happening.
Because RoadGenerator is a surface populator, the same kind of generator as the one that adds the flowers to the world. As a result, it is likely that the flora surface populator is running before the RoadGenerator (and it generates based on what block is below the potential flora which will be grass when it runs), so the RoadGenerator is replacing grass blocks that already have flowers on top with asphalt, breaking the flowers.