While I can't know precisely what the others mean, in general what is meant by the GPU being overkill is that, buying a top tiered card for use at a 1080p resolution is going to be spending money to buy a lot more graphics horsepower than you are going to be able to enjoy. A GTX 1080 is more than is necessary to get 60 fps in many titles at that resolution, with the bells and whistles turned up. Of course, this also is going to depend on the rest of your system, whether it can keep the card fed fast enough to maintain the high frame rates during games.
As far as bottlenecks, these too are not harmful. All computers have bottlenecks, or you would get infinite performance. The bottleneck is simply the point at which a part is being used to it's fullest, and can not perform faster, causing other parts to have to wait for it. Depending on software conditions and hardware present, this usually goes back and forth between the CPU and the GPU. In some games, the CPU is the limiting factor, in some, the GPU. This can also be influenced by the graphics settings chosen.
Now, is this harmful? Not at all, in the least, in the most, with cheese or on toast. This is not a moral issue, and there is nothing wrong if you want to do this. Provided the graphics card runs fine in your computer, you can run it all day long at any resolution it supports and you won't do any harm to it. You just may not end up getting the full utility from a high end graphics card by using it at 1080p, but you certainly won't be hurting anything.
On the other hand, if you are going to be using a 144 Hz or faster monitor, the GTX 1080 will often still not be enough to guarantee you never fall below your maximum refresh, even at 1080p.