I had a pre-finished engineered european oak floor installed and I believe some of the installed planks have severe defects. See pictures.

http://imgur.com/a/h50de

This is a floating floor installation (glued tongue and groove) over rubber underlayment (required by HOA for 2nd floor condo).

I am talking to the installer about what to do about these boards. Is it safe to ask him to just replace all these boards or will it just get worse? Or is there something else we can do to fix these issues? The variation in grade was substantially more than we expected but we do like the look except I am worried about the open voids, among other things.

If you use linseed oil putty which will be soft and take a lot of time to harden, dirt or other surface contaminants will make it look ugly.
There is a putty that was made especially for pre-finished flooring. It is made by Woodwise and comes in different colors. It's water-based and will shrink a little as it dries in a deep crack. It has a little shine as it's buffed when dry with a soft cloth but won't match a "satin" finish perfectly.
It comes with directions on the small bottles.

I met with the installer today and they agreed to replace all these planks except for the one with the knot hole in it which should be easily filled. I will check out the woodwise filler. Thanks!