Self leveling showing popped bubbles and small chunks
I just did my concrete floor for vinyl plank, and I would be concerned more for the flatness the the floor that it is within the tolerances needed. The bumps can be scraped off, at worst ground off. When I poured mine, I had high spots that needed ground down, quite the dusty job. The holes in  the mix from the air bubbles will be of no concern, the flooring will span over them with no problem. 

You may also find that the lumps are just unpopped air bubbles.