Office warns me my changes will be lost and offers to change to XLSX. Numbers just changes it silently, without warning.
Yes, the Numbers program saved it as a Numbers document.
Just like Excel saves Excel files.
That's why it's called "import," not "open."
When you pressed Save, a Save As dialog popped up asking for a name. If you had just saved it to the same file, there would be no Save As dialog. It wouldn't ask you for a name because it knew the name.
This is standard across every app on every Mac going back decades. I don't use Windows very often, but I believe it's the same there, too. You aren't asked for a filename if you're updating the same file.
It doesn't sound like an Apple problem, it sounds like you didn't pay attention, and when the computer did what you asked, you blamed the computer. There's nothing Apple or Microsoft or anyone else can do about that.
Not if, like the OP, you open a CSV file first, then hit save.
If you're just editing some values, you can save back to CSV with CTRL+S no problems.
They have a small banner at the top to warn about this, but it doesn't even address the things that were already lost the instant you opened it.
Excel does save back to CSV. It discards half your changes because they can't be saved in a CSV, modifies anything that could possibly be a date, and rounds random numbers, THEN it saves it as a CSV.
Numbers makes this an explicit "Export" option because silently saving these types of changes is super dangerous.
I wish they'd warn you on first operation that CSV can't handle, and ask.