It's not about pipes
As the answer to your linked question states,
By default, spells do not work without clear line of sight. Therefore, a solid pipe blocks spells, regardless of the construction material
So, you cannot target the water in those pipes, unless the pipe has an open end or faucet, where it is openly accessible. Not because the game cares about pipes, but because that is how the spellcasting rules work.
Whatever the exact definitions of "freestanding", "an area of water" or "an open container" amount to, while we do not know the reasons why the designers wrote the spells this way, we can guess that it is likely to avoid abuse against living beings. As about 60% of the human body is made of water, you otherwise would get into all kinds of discussion if you can control an opponent's body, by controlling the water it is made up from, or if you can kill an opponent, by destroying the water in their body. This obviously is not what those spells are designed to do.
That this may have a collateral effect on water in pipes, even if the pipe has an open end, is likely just that, an unintended side effect. As all these terms are no further defined, what it will come down to in the end is how your DM interprets those terms.
What freestanding water is discussed in the linked question. Either, water not chemically bonded, or water in a pool, river, lake etc, water not held in a structure. As control water also talks about an area, my take it means lakes and the like, but your DM may have a different read.
A container is defined by Oxford Languages as a portable compartment, so a pipe would not be a good fit for it, unless it was detached and could be carried around. But of course, the pipes do contain water, so if it is open at one end, the DM might decide you can affect water that you can target, and stretch the definition of container to allow this.
a : a receptacle (such as a box or jar) for holding goods
b : a portable compartment in which freight is placed (as on a train or ship) for convenience of movement
- What is an area of water? The term area is likewise not further defined by the rules (although they do define what Areas of Effect are). Again according to Oxford languages:
the surface included within a set of lines; specifically: the number of unit squares equal in measure to the surface
The spell says
You choose an area of water that you can see within range and that fits within a 5-foot cube.
which means you need to be able to see the water, and due to spellcasting rules, and you need line of effect to target it. The term area by the dictionary definition here does not really make a lot of sense, because you of course do not target and affect only the 2-dimensional surface of the water, you affect the actual 3-dimensional volume. Again, if your DM decides that you can target the water because there is an exposed end to the pipe, and if the pipe is transparent so you can see the water, you might be able to affect the water within the pipes that fits within a 5-foot cube.