As you point out, the normal way to do this would be using BOTH a rule above and a rule below, such as:

But you’re right that you cannot do this over colored backgrounds!

Hm. I can’t think of any good way around that. Anyone else?

If the lines still appear when you turn on Preview, then they almost certainly WILL print!
My guess is that you have the Underline feature turned on. Perhaps there is a character style applied? (Look in the Character Style panel. Or, select the text and see if the Underscore button is turned on in the Control panel.)

Sorry, I’ve never heard of JATS XML. This forum is really focused on how to use InDesign to create EPUB.

I haven’t heard of any changes, but that does sound really weird. These are QR codes made with data merge? If you make them manually (from nothing) do they work okay?

That IS strange. Have you tried exporting the file as IDML and then opening that IDML file? That might clear up some corruption or something.

Also, make sure the Dictionary pane of the Preferences dialog box is set the same as yours.

Here’s more ideas:
https://creativepro.com/why-red-squiggly-underlines-when-words-are-not-spelled-wrong.php

As Janet pointed out, you can do this with spans, as shown here:
https://creativepro.com/adding-space-above-below-lists-span-column.php