Repairing ball marks in your line of play?

You may fix ball marks on the green without restriction.  Your ball does not have to be on the green.  This will indeed improve your line of putt or line of play, or your lie.  That's the whole idea for doing it in the first place. This is allowed under these circumstances.

FYI, Obstructions are artificial things like roads, paths, etc.  and there is a separate rule for these.  Divots or ball marks are not obstructions.

Yes, you can (and should) repair any and all ball marks you see on the green.  As long as you aren't testing the surface of the green with your hand or fingers when repairing the ball mark it is perfectly legal.  I want to say spike marks are not allowed to be fixed if in your line of play but may be fixed afterwards, but I may be wrong on that.  I think that is why sometimes when watching the PGA on TV you will see a player call his playing partner in to decipher whether it is a ball mark or spike mark.

Spike marks may not be touched if doing so will assist in your subsequent play of the hole, or your partner's play.  This normally covers areas just past the hole on your line of putt.

Also, you may not touch your line of putt or improve your line of putt by pressing anything down.  This covers spike marks between the ball and the hole.

There are exceptions to touching your line of putt,  ball marks being one of them.

After everyone in your group has holed out, you are free to repair spike marks, without restriction, and is good course etiquette.

Also I don't see how one could be in breach of R16-1d (Testing Surface) when fixing a ball mark.

Edit:  Ok, maybe if your are doing something really weird with your fingers.

You are in fact quite correct.