You can run a pond without a mechanical filter. Plants roots can do the job, you just need to add the plants and lots of them (I believe it's called a biological filter). Keep in mind I am new and haven't even filled my pond yet so I am just telling you what I have read ;) As for the fish, I would use the pond water to fill the pools to prevent shock and put some sort of air stone or something in the pools to create bubbles or the fish might die. There are many helpful people on here that I am sure will be posting more detailed and useful information soon.

I would try first to tighten the flange on the bottom of the drain connection, if it still leaks, you could try replacing the gasket, I wouldn't go replaceing the whole drain valve just for the leak, unless you found that it was cracked.

If this is new construction, which because of your "home builder" comment, I'm guessing it is...then I doubt if it's a tile-over. Clamping drains are a threaded design, so the body can be raised or lowered as needed to get the correct elevation. Either someone didn't know what they were doing, or someone didn't know what they were doing. But they certainly knew how to fake it. You can certainly try to pull an explanation out of your builder. In general, the plumber is in charge of installing the drain and the shower pan membrane. The tiler is in charge of setting the drain height and building up the pan and tiling the pan. Sometimes continents collide and job paths get cross-contaminated. But in the end, your home builder is responsible for the action of his subs, however convoluted those cations may be. You can pursue this however you choose. I'm not normally one to recommend patch repairs. However, if you've had no negative issues with the floor; how it drains, how it dries? It might be best to leave things be. I say that with the exception of having to provide some form of proper support for the top drain grate. It might be best to remove the screws that hold the bottom grate, get longer screws, and install the top grate with the longer screws into the screw holes of the bottom grate. That'll secure the top grate to the drain body below. You can sleeve the screws between the two grates to provide support for the top grate with a 1/4" sleeve to fill the gap between the two grates. Perimeter support for the top grate can be added as needed.

Can you take a photo of the floor of the shower? What I suspect is this isn't a plumbing problem. I suspect it's a shower pan / tile problem.