My greater concern here would be "Dynamic Pressure" which is the working pressure under flow. This bathroom is on the third floor so if this structure is on slab the vertical rise from the water main to the shower mixer will be approximately 24' and with a basement it could be as much as 32' or perhaps more. That would be a 10.3 to 13.8psig loss to vertical head. While the code required minimum dynamic head pressure for a standard shower mixer is only 8psig a temperture controlled shower mixer is required a minimum 20psig dynamic pressure. This means you would need between 30.3 and 33.8psig dynamic pressure at the main under full flow.

I certainly hope you don't plan on ever selling that house. If a sharp eyed inspector sees the line configured like that or the pipe in the crawl space just resting on the ground without code approved supports they will list your plumbing as not conforming to code and it could be a real sticking point with the future buyer or a lending institute. Code prohibits using a vertical section of pipe as a support for a horizontal line. PVC pipe is required to have a support hanger within one foot of a major change in direction and at least one ever four linear feet. The hangers are required to be made of plastic or you may use plastic perf strapping. Metal or wire hangers are strictly prohibited.

The staining may only be happening in a few boards but the CUPPING of the planks is more wide spread. That's the biggest issue. As for moisture mitigation during install, it would be up to you to contact the original installer to find out what was done. Only they can answer those questions for you. But I will give you a heads up on that one. These OLD slabs (1948 = post war era building boom) are often thought of as DRY when carpet is removed (again, this is why I asked what USED to be on the floor). The slab will 'test' as dry because it has been happily evaporating off moisture THROUGH the carpet for decades. And decades. And decades. Many moisture tests (ie. anhydrous calcium chloride test) will see how much PRESSURE is in the slab on that day. If carpet is removed and there is NO BUILD-UP of moisture/pressure BEFORE that day, it will 'read' as a nice dry-ish slab. Once the slab is CAPPED (solid flooring put over top = nowhere for the water to escape = HIGH moisture content/pressure) it gets MUCH more difficult to deal with. If you test the slab TODAY it will be MUCH HIGHER than the slab was before you put the wood on it. The moisture barrier treatment at the TIME was 'good enough' for the reading (3 years ago before the slab filled with water). But NOW the moisture has overwhelmed the system used. This is why it takes wet-basement specialists to figure out some of these old slabs. The moisture tests done before they were capped probably looked very good (or very promising to be good in the future) but the wood flooring people could not predict the pressure build up over 3 years. That's not their level of expertise. A wet-slab/basement specialist *MIGHT have been able to guestimate the issues...but they too might have guessed wrong. These old slabs are SUPER TRICKY to predict. Please tell us if your floors are glued down to the concrete or if they are floating. Please add more photos of the cupping please. Tell us how much of the 1800sf is having moisture issues (cupping/staining, popping, etc).

You can cut off and cap the copper pipes coming out of the floor, but I'd first try to figure out where they are coming from. You don't someone turning a shutoff in the basement or crawl space (I wonder what this does?) and finding out it controls the water line running to this pipe. Smaller sizes of cast iron pipe usually have threaded fittings, while large waste pipes may use oakum and lead for the seal. Old cast iron pipes are usually fine for vertical runs (vent stacks, etc.), but horizontal iron pipe runs trap moisture and form rust in the bottom (looks like stalagmites). This rust catches on whatever is draining through the pipe (hair, soap, etc.) and creates a blockage over time. A plumbers snake becomes your friend. The rubber fittings are usually called Fernco couplings, since its the most common manufacturer of this type of coupler. They are used to connect dissimilar pipes during renovation (iron pipe to PVC, etc.), or to reconnect a pipe that has been cut. There is nothing wrong with using them if the pipe is adequately supported on both sides of the rubber coupling. Bruce