I'm with you on wanting to address the cover not meeting the concrete squarely. However, sometimes the fix is worse than the issue. I get that it's not square and you notice it. But functionally, it's not much of an issue. Theoretically some debris could go in that area, but not that much likely. I think cutting the concrete square will make it look different in that you'll see all the stones in the concrete cut flat. I know you mention tiling to cover it, but I would have a few big reservations about that plan. If you don't do it to all four coping edges, it's going to look weird. Much more weird than a slight gap. If you do choose to tile, I'm not sure I understand you comment about tiling the deck. You can't tile a deck as it will result in needing to create a dedicated highway lane from your house to the local E.R. to repair all the broken bones from slip/fall accidents. Maybe I missed something on that aspect though. Another concern is if there is any metal in the concrete close to the edge. Probably not, but if there is, that will be a problem unless it's tiled over as you mention. Adding a bumper to the leading edge bar is going to give you something to also be focused on and displeased with anytime the cover is open and you are enjoying the pool - which wouldn't be on your wish list either.
Bottom line is you have something that's not quite right, but any method to fix it that I can think of, spans from hokey to problematic.
I too have an autocover. Our pool coping is perfectly square. However, the leading edge bar is slightly concave in the middle allowing a 1/2" gap at that point which narrows to nothing at either end. So I do have some perspective on the issue leading to my comments above.
Just food for thought as I know when in the heat of not being happy, everything gets magnified and "must" be fixed. Every other issue that you've had to deal with on the pool somehow affects our insight on any particular issue.
I agree on just using caulk to fill in that small gap. Seems like such a simple solution with little downside. If it looks bad down the road, scrape it out and reapply.