One of the options we recommend for vias in BGA pads is to have them filled and plated over. You can have this done at the your board house for full vias or microvias. If done properly, it effectively takes the via out of consideration. It doesn't matter any more.
However, sometimes the processing isn't nailed down and you can get either a indent or small bump over the filled via. The indent is probably most common when resin is used to fill the via. In either case, the bump or dip can lead to a less reliable assembly, especially with fine pitch BGAs and chip scale packages.
There's always just one more thing. Isn't there.
So, if you are going to put vias in your BGA pads, our first recommendation is to have them filled and plated over at the board house. If you do that, make sure you discuss it with them and see what their standards are for creating a planar surface.
You can probably tell, but I simulated the bump and dip in these images. I don't have good real examples, but this is pretty much what it would look like.