I think everything makes sense for the most part. What I was seeing was in the editor, when I opened my existing save and copied/pasted existing underground pipes, the newly placed pipes would appear normally but then disappear. And this I think is what confused me.
Now, one thing I do see specifically on my existing save is that when I copy and paste an existing segment, the newly placed segment appears as an alternating sequence of placed and "ghost" pipes. One will be blue and one will be normal colored semitransparent. The fluid icon will be there regardless, and they will all disappear, but it's almost as if half of them are ghosts and half are real. But, they all end up there in the end.
Regardless, I don't think this issue is worth pursuing because my save game is an unholy hodgepodge of changing mods in a game that dates back to Factorio v1, so I don't think it's worth creating an issue for unless you are simply bored and want to cause grief for yourself.