First good luck. I have been sorely disappointed in my Retrax and would not but another one, especially considering the comparative cost. But to your concerns.
The indention looks like it could be caused be the little spike that locks the cover to the rail. When closed, there really shouldn't be much play in the top. The bolt in the picture sticking out from the rail hold the cover in the fully closed position.
From the pictures and your description, your rail(s) need to be solid toward the tailgate. That should help cost the gap at the tailgate.
Now, that gap in the front. I bought a cover late 2017 when I bought my truck. It didn't have a gap there, ever. Ended up getting a warranty replacement for water intrusion through the rubber seals between the slats. Now I have a gap at the front. It appears they changed the length of the cover (warranty replaced cover only, not rails). No clue how to fix. I need to take my cover back off and I intend to put something to cover the hole in the back of the canister. When it rains and I'm driving the front wall of my bed gets completely soaked from wind driving rain through that gap and out the bank of the canister.
For water around the edges of the bed. This ticks me off now than anything and should have been solved by rail design, but it's not and I'm not certain there's a good way to keep it working long term. When installing the rails, you actually have to twist the rails up, to secure them at an forward angle. This directs water that gets in the channel where the wheels run to for away from the bed. Don't worry, due to surface tension it'll still hug the cover and drip down some in your bed. You'll really need the white nylon studs mentioned earlier to get this right. They actually updated their instructions at find point; the original printed instructions that came with my cover didn't mention it.
Good luck!